rs2960420

Variant names:

• chr3-12273013-C-G
• rs2960420

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 0.407 in 152,020 control chromosomes in the GnomAD database, including 13,143 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 0.41 (13143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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: 0.407 AC: 61792 AN: 151904 Hom.: 13122 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.407 AC: 61855 AN: 152020 Hom.: 13143 Cov.: 32 AF XY: 0.409 AC XY: 30372 AN XY: 74292

African (AFR) AF: 0.518 AC: 21469 AN: 41460

American (AMR) AF: 0.349 AC: 5332 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2139 AN: 5168

South Asian (SAS) AF: 0.560 AC: 2700 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4105 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23677 AN: 67972

Other (OTH) AF: 0.384 AC: 808 AN: 2104

Alfa AF: 0.376 Hom.: 1543

Bravo AF: 0.403

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2960420; hg19: chr3-12314512;