10-57429418-T-C

Variant names:

• chr10-57429418-T-C
• rs4462262

Variant summary

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

The variant allele was found at a frequency of 0.556 in 151,806 control chromosomes in the GnomAD database, including 24,834 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 0.56 (24834 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84405 AN: 151688 Hom.: 24827 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.556 AC: 84443 AN: 151806 Hom.: 24834 Cov.: 31 AF XY: 0.563 AC XY: 41744 AN XY: 74188

African (AFR) AF: 0.368 AC: 15258 AN: 41426

American (AMR) AF: 0.631 AC: 9629 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3468

East Asian (EAS) AF: 0.940 AC: 4846 AN: 5154

South Asian (SAS) AF: 0.576 AC: 2774 AN: 4820

European-Finnish (FIN) AF: 0.649 AC: 6845 AN: 10544

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41134 AN: 67818

Other (OTH) AF: 0.559 AC: 1177 AN: 2106

Alfa AF: 0.593 Hom.: 98263

Bravo AF: 0.548

Asia WGS AF: 0.716 AC: 2486 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.85
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4462262; hg19: chr10-59189178;