chr2-161032682-T-C

Variant names:

• chr2-161032682-T-C
• rs2551691

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 0.837 in 152,174 control chromosomes in the GnomAD database, including 53,825 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 0.84 (53825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.838 AC: 127372 AN: 152054 Hom.: 53804 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.837 AC: 127420 AN: 152174 Hom.: 53825 Cov.: 32 AF XY: 0.837 AC XY: 62315 AN XY: 74410

African (AFR) AF: 0.712 AC: 29515 AN: 41478

American (AMR) AF: 0.879 AC: 13438 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2923 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5169 AN: 5190

South Asian (SAS) AF: 0.866 AC: 4177 AN: 4822

European-Finnish (FIN) AF: 0.859 AC: 9094 AN: 10588

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60452 AN: 68014

Other (OTH) AF: 0.828 AC: 1752 AN: 2116

Alfa AF: 0.874 Hom.: 85632

Bravo AF: 0.836

Asia WGS AF: 0.913 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs2551691; hg19: chr2-161889193;