2-83432543-G-A

Variant names:

• chr2-83432543-G-A
• rs981525

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 0.457 in 151,948 control chromosomes in the GnomAD database, including 16,463 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 0.46 (16463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 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 = 0.806 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: 0.457 AC: 69324 AN: 151830 Hom.: 16445 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.457 AC: 69388 AN: 151948 Hom.: 16463 Cov.: 32 AF XY: 0.460 AC XY: 34139 AN XY: 74278

African (AFR) AF: 0.427 AC: 17712 AN: 41436

American (AMR) AF: 0.570 AC: 8694 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1438 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4258 AN: 5150

South Asian (SAS) AF: 0.434 AC: 2096 AN: 4828

European-Finnish (FIN) AF: 0.407 AC: 4297 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29269 AN: 67928

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.450 Hom.: 19019

Bravo AF: 0.474

Asia WGS AF: 0.643 AC: 2232 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.079
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs981525; hg19: chr2-83659667;