2-119129830-G-T

Variant names:

• chr2-119129830-G-T
• rs10496556

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.561 in 152,102 control chromosomes in the GnomAD database, including 24,764 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 0.56 (24764 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 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: 0.561 AC: 85274 AN: 151984 Hom.: 24761 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.561 AC: 85308 AN: 152102 Hom.: 24764 Cov.: 33 AF XY: 0.564 AC XY: 41938 AN XY: 74380

African (AFR) AF: 0.438 AC: 18149 AN: 41450

American (AMR) AF: 0.572 AC: 8747 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2329 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1612 AN: 5178

South Asian (SAS) AF: 0.659 AC: 3177 AN: 4824

European-Finnish (FIN) AF: 0.665 AC: 7036 AN: 10586

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42531 AN: 67992

Other (OTH) AF: 0.568 AC: 1198 AN: 2108

Alfa AF: 0.616 Hom.: 16840

Bravo AF: 0.540

Asia WGS AF: 0.440 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs10496556; hg19: chr2-119887406;