rs983970

Variant names:

• chr2-125383270-G-A
• rs983970

Your query was ambiguous. Multiple possible variants found:

• chr2-125383270-G-A
• chr2-125383270-G-T

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 0.483 in 149,568 control chromosomes in the GnomAD database, including 18,314 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 0.48 (18314 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.483 AC: 72136 AN: 149478 Hom.: 18300 Cov.: 28

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.483 AC: 72189 AN: 149568 Hom.: 18314 Cov.: 28 AF XY: 0.490 AC XY: 35659 AN XY: 72734

African (AFR) AF: 0.354 AC: 14372 AN: 40596

American (AMR) AF: 0.575 AC: 8628 AN: 15016

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1999 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4410 AN: 5106

South Asian (SAS) AF: 0.624 AC: 2970 AN: 4758

European-Finnish (FIN) AF: 0.497 AC: 4795 AN: 9648

Middle Eastern (MID) AF: 0.628 AC: 182 AN: 290

European-Non Finnish (NFE) AF: 0.493 AC: 33350 AN: 67694

Other (OTH) AF: 0.533 AC: 1114 AN: 2090

Alfa AF: 0.495 Hom.: 3344

Bravo AF: 0.481

Asia WGS AF: 0.736 AC: 2555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs983970; hg19: chr2-126140847;