10-124272929-A-G

Variant names:

• chr10-124272929-A-G
• rs4962394

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 0.288 in 151,948 control chromosomes in the GnomAD database, including 7,462 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 0.29 (7462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 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 = 0.564 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43749 AN: 151830 Hom.: 7442 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.288 AC: 43797 AN: 151948 Hom.: 7462 Cov.: 32 AF XY: 0.295 AC XY: 21882 AN XY: 74272

African (AFR) AF: 0.129 AC: 5328 AN: 41450

American (AMR) AF: 0.397 AC: 6067 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2995 AN: 5152

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4804

European-Finnish (FIN) AF: 0.362 AC: 3817 AN: 10546

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21476 AN: 67936

Other (OTH) AF: 0.318 AC: 669 AN: 2104

Alfa AF: 0.316 Hom.: 12557

Bravo AF: 0.287

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.58
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs4962394; hg19: chr10-125961498;