rs2922126

Variant names:

• chr3-172449471-T-A
• rs2922126

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 0.28 in 151,948 control chromosomes in the GnomAD database, including 6,959 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 0.28 (6959 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.280 AC: 42468 AN: 151828 Hom.: 6954 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.280 AC: 42480 AN: 151948 Hom.: 6959 Cov.: 31 AF XY: 0.286 AC XY: 21228 AN XY: 74274

African (AFR) AF: 0.102 AC: 4234 AN: 41448

American (AMR) AF: 0.292 AC: 4467 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2294 AN: 5144

South Asian (SAS) AF: 0.438 AC: 2107 AN: 4816

European-Finnish (FIN) AF: 0.399 AC: 4212 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22853 AN: 67928

Other (OTH) AF: 0.309 AC: 653 AN: 2114

Alfa AF: 0.303 Hom.: 939

Bravo AF: 0.261

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.57
DANN	Benign	0.51
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2922126; hg19: chr3-172167261;