rs2901822

Variant names:

• chr10-94924679-T-A
• rs2901822

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 0.0494 in 152,162 control chromosomes in the GnomAD database, including 247 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 0.049 (247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7522 AN: 152044 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0494 AC: 7515 AN: 152162 Hom.: 247 Cov.: 32 AF XY: 0.0499 AC XY: 3716 AN XY: 74404

African (AFR) AF: 0.0125 AC: 518 AN: 41580

American (AMR) AF: 0.0487 AC: 744 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5174

South Asian (SAS) AF: 0.114 AC: 552 AN: 4828

European-Finnish (FIN) AF: 0.0560 AC: 593 AN: 10584

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4470 AN: 67952

Other (OTH) AF: 0.0527 AC: 111 AN: 2108

Alfa AF: 0.0571 Hom.: 32

Bravo AF: 0.0461

Asia WGS AF: 0.0780 AC: 271 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.58
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2901822; hg19: chr10-96684436;