rs2001795

Variant names:

• chr2-22892664-T-C
• rs2001795

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 0.541 in 152,022 control chromosomes in the GnomAD database, including 22,597 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 0.54 (22597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 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: 0.541 AC: 82130 AN: 151904 Hom.: 22567 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.541 AC: 82205 AN: 152022 Hom.: 22597 Cov.: 32 AF XY: 0.540 AC XY: 40101 AN XY: 74288

African (AFR) AF: 0.541 AC: 22408 AN: 41436

American (AMR) AF: 0.568 AC: 8686 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1324 AN: 5168

South Asian (SAS) AF: 0.501 AC: 2412 AN: 4812

European-Finnish (FIN) AF: 0.576 AC: 6094 AN: 10580

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37438 AN: 67958

Other (OTH) AF: 0.529 AC: 1118 AN: 2114

Alfa AF: 0.545 Hom.: 57848

Bravo AF: 0.543

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2001795; hg19: chr2-23115536;