2-125855650-T-G

Variant names:

• chr2-125855650-T-G
• rs6751266

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 0.79 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.775 AC: 32114 AN: 41420

American (AMR) AF: 0.644 AC: 9835 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2746 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1074 AN: 5130

South Asian (SAS) AF: 0.622 AC: 2993 AN: 4814

European-Finnish (FIN) AF: 0.898 AC: 9522 AN: 10598

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59190 AN: 67976

Other (OTH) AF: 0.771 AC: 1629 AN: 2112

Alfa AF: 0.795 Hom.: 17415

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6751266; hg19: chr2-126613227;