2-183861755-T-C

Variant names:

• chr2-183861755-T-C
• rs826161

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 0.891 in 152,042 control chromosomes in the GnomAD database, including 60,534 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 0.89 (60534 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135403 AN: 151926 Hom.: 60481 Cov.: 30

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.891 AC: 135514 AN: 152042 Hom.: 60534 Cov.: 30 AF XY: 0.893 AC XY: 66361 AN XY: 74340

African (AFR) AF: 0.920 AC: 38175 AN: 41512

American (AMR) AF: 0.899 AC: 13727 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2815 AN: 3462

East Asian (EAS) AF: 0.968 AC: 4993 AN: 5158

South Asian (SAS) AF: 0.906 AC: 4367 AN: 4820

European-Finnish (FIN) AF: 0.863 AC: 9080 AN: 10522

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59443 AN: 67980

Other (OTH) AF: 0.876 AC: 1845 AN: 2106

Alfa AF: 0.896 Hom.: 4853

Bravo AF: 0.895

Asia WGS AF: 0.918 AC: 3186 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs826161; hg19: chr2-184726482;