2-125855650-T-G

Position:

• chr2-125855650-T-G

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 0.79 in 152,000 control chromosomes in the GnomAD database, including 49,026 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 0.79 (49026 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120035 AN: 151882 Hom.: 48994 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.790 AC: 120109 AN: 152000 Hom.: 49026 Cov.: 31 AF XY: 0.781 AC XY: 57985 AN XY: 74286

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.771

Alfa AF: 0.821 Hom.: 9533

Bravo AF: 0.766

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6751266; hg19: chr2-126613227;