2-76495179-T-C

Variant names:

• chr2-76495179-T-C
• rs17012789

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 0.162 in 151,854 control chromosomes in the GnomAD database, including 2,690 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 0.16 (2690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.162 AC: 24653 AN: 151736 Hom.: 2694 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.162 AC: 24656 AN: 151854 Hom.: 2690 Cov.: 32 AF XY: 0.165 AC XY: 12259 AN XY: 74192

Gnomad4 AFR AF: 0.0535

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.183

Alfa AF: 0.183 Hom.: 1317

Bravo AF: 0.166

Asia WGS AF: 0.374 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17012789; hg19: chr2-76722305;