2-192275657-G-A

Variant names:

• chr2-192275657-G-A
• rs2581226

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 0.819 in 150,816 control chromosomes in the GnomAD database, including 50,977 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 0.82 (50977 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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: 0.819 AC: 123406 AN: 150696 Hom.: 50936 Cov.: 26

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.819 AC: 123504 AN: 150816 Hom.: 50977 Cov.: 26 AF XY: 0.816 AC XY: 60032 AN XY: 73568

African (AFR) AF: 0.898 AC: 36772 AN: 40936

American (AMR) AF: 0.767 AC: 11577 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2747 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2561 AN: 5122

South Asian (SAS) AF: 0.808 AC: 3844 AN: 4756

European-Finnish (FIN) AF: 0.792 AC: 8181 AN: 10330

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55151 AN: 67812

Other (OTH) AF: 0.790 AC: 1650 AN: 2088

Alfa AF: 0.822 Hom.: 6032

Bravo AF: 0.814

Asia WGS AF: 0.717 AC: 2493 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.27
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2581226; hg19: chr2-193140383;