2-176120968-T-C

Variant names:

• chr2-176120968-T-C
• rs711819

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.814 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

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.813

Alfa AF: 0.788 Hom.: 70231

Bravo AF: 0.820

Asia WGS AF: 0.637 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs711819; hg19: chr2-176985696;