rs10492757

Variant names:

• chr16-7724637-A-C
• rs10492757
• ENST00000777597.1:n.403-31176T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777597.1(ENSG00000301273):​n.403-31176T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,164 control chromosomes in the GnomAD database, including 1,668 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1668 hom., cov: 32)
• Consequence: ENSG00000301273 ENST00000777597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

ENSG00000301273 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301273	ENST00000777597.1	n.403-31176T>G		intron_variant	Intron 3 of 3
ENSG00000301273	ENST00000777598.1	n.311-31176T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21172 AN: 152046 Hom.: 1664 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.137

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.139 AC: 21213 AN: 152164 Hom.: 1668 Cov.: 32 AF XY: 0.136 AC XY: 10107 AN XY: 74402

African (AFR) AF: 0.216 AC: 8954 AN: 41498

American (AMR) AF: 0.0954 AC: 1459 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3470

East Asian (EAS) AF: 0.00965 AC: 50 AN: 5182

South Asian (SAS) AF: 0.118 AC: 568 AN: 4826

European-Finnish (FIN) AF: 0.0618 AC: 655 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8348 AN: 67980

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.130 Hom.: 1991

Bravo AF: 0.144

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10492757; hg19: chr16-7774639;