2-176120968-T-C

Variant names:

• chr2-176120968-T-C
• rs711819

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 0.814 in 152,180 control chromosomes in the GnomAD database, including 51,187 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 0.81 (51187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123704 AN: 152062 Hom.: 51126 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.814 AC: 123824 AN: 152180 Hom.: 51187 Cov.: 32 AF XY: 0.813 AC XY: 60472 AN XY: 74378

African (AFR) AF: 0.933 AC: 38729 AN: 41526

American (AMR) AF: 0.828 AC: 12653 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2117 AN: 5170

South Asian (SAS) AF: 0.840 AC: 4052 AN: 4824

European-Finnish (FIN) AF: 0.779 AC: 8258 AN: 10600

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52523 AN: 67990

Other (OTH) AF: 0.813 AC: 1716 AN: 2110

Alfa AF: 0.791 Hom.: 96973

Bravo AF: 0.820

Asia WGS AF: 0.637 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs711819; hg19: chr2-176985696;