2-126986712-G-C

Variant names:

• chr2-126986712-G-C
• rs477449

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 0.513 in 151,942 control chromosomes in the GnomAD database, including 21,684 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 0.51 (21684 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 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: 0.514 AC: 77996 AN: 151824 Hom.: 21679 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.513 AC: 78003 AN: 151942 Hom.: 21684 Cov.: 31 AF XY: 0.510 AC XY: 37881 AN XY: 74264

African (AFR) AF: 0.291 AC: 12046 AN: 41442

American (AMR) AF: 0.506 AC: 7735 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3468

East Asian (EAS) AF: 0.656 AC: 3381 AN: 5156

South Asian (SAS) AF: 0.401 AC: 1930 AN: 4816

European-Finnish (FIN) AF: 0.557 AC: 5867 AN: 10536

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43005 AN: 67940

Other (OTH) AF: 0.526 AC: 1105 AN: 2102

Alfa AF: 0.568 Hom.: 3137

Bravo AF: 0.505

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.82
DANN	Benign	0.75
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs477449; hg19: chr2-127744288;