Pubvar

12:103232363:T/C

GRCh37/hg19 position	12:103232363
GRCh38/hg38 position	12:102838585
Alleles (ref/alt)	T/C
dbSNP rsid	rs536759523
Gene symbol	PAH
Most severe consequence	3_prime_UTR_variant
Flanking sequence	GTTTTATTACCTTATACAGCAGTATTTATGA[T/C]TACAATAAAACATACAAAAATGTTTTTATAT
HGVS	NM_000277.3:c.590A>G NM_001354304.2:c.590A>G

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Gene annotations

Transcript	Gene	Exon number	Consequence	HGVS cDNA	HGVS protein	Location	Protein location
NM_000277.3	PAH	13	3_prime_UTR_variant	c.*590A>G	-	3' UTR
NM_001354304.2	PAH	14	3_prime_UTR_variant	c.*590A>G	-	3' UTR

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Population frequency

Select populations: ALL LWK MKK YRI EUR FIN NFE CEU ASJ TSI EAS SAS CHB HAN CHD JPT AFR AMR ASW GIH MEX OTH

Database	Population	AC	AN	Hom	AF
1000 genomes	ALL	1	5008	-	0.000199681
	EUR	-	-	-	0
	EAS	-	-	-	0
	SAS	-	-	-	0
	AFR	-	-	-	0.0008
	AMR	-	-	-	0
gnomAD genomes	ALL	9	30952	0	0.000290773
	FIN	0	3478	0	0
	NFE	0	15006	0	0
	ASJ	0	302	0	0
	EAS	0	1618	0	0
	AFR	9	8734	0	0.00103046
	AMR	0	836	0	0
	OTH	0	978	0	0

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View on UCSC genome browser

Conservation

Conservation scores are retrieved from UCSC genome browser. The conservation levels are defined by simple cutoff values. If the conservation levels do not agree with each other, you can manually check whether this variant is conserved with UCSC genome browser.

Method	Score	Level
GERP++	-1.01	Not conserved
phastCons46way primates	0.018	Not conserved
phastCons46way placental	0.018	Not conserved
phastCons100way vertebrates	0	Not conserved
phyloP46way primates	0.477	Not conserved
phyloP46way placental	-0.16	Not conserved
phyloP100way vertebrates	-0.227	Not conserved

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InterVar

InterVar is a software tool for clinical interpretation of genetic variants by the ACMG/AMP 2015 guideline. The eveidence tags that variant met are highlighted. Please note that evidence tags with need to be evaluated manually.

Class: Uncertain significance

	Benign		Pathogenic
	Strong	Supporting	Supporting	Moderate	Strong	Very Strong
Population data	BA1 BS1 BS2			PM2	PS4
Computational and predictive data		BP1 BP3 BP4 BP7	PP3	PM4 PM5	PS1	PVS1
Functional data	BS3		PP2	PM1	PS3
Segregation data	BS4		PP1	PP1	PP1
De novo data				PM6	PS2
Allelic data		BP2		PM3
Other database		BP6	PP5
Other data		BP5	PP4