chr10-131499926-G-A

Variant names:

• chr10-131499926-G-A
• rs4074863

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 0.269 in 152,124 control chromosomes in the GnomAD database, including 5,612 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 0.27 (5612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 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: 0.269 AC: 40910 AN: 152006 Hom.: 5609 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.269 AC: 40920 AN: 152124 Hom.: 5612 Cov.: 33 AF XY: 0.266 AC XY: 19749 AN XY: 74362

African (AFR) AF: 0.305 AC: 12649 AN: 41466

American (AMR) AF: 0.218 AC: 3335 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1587 AN: 5158

South Asian (SAS) AF: 0.189 AC: 912 AN: 4822

European-Finnish (FIN) AF: 0.218 AC: 2316 AN: 10604

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17847 AN: 68002

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.270 Hom.: 1699

Bravo AF: 0.276

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4074863; hg19: chr10-133298189;