2-125345109-C-T

Variant names:

• chr2-125345109-C-T
• rs313264

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 0.521 in 151,856 control chromosomes in the GnomAD database, including 22,163 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 0.52 (22163 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79122 AN: 151738 Hom.: 22131 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.521 AC: 79192 AN: 151856 Hom.: 22163 Cov.: 31 AF XY: 0.510 AC XY: 37827 AN XY: 74216

African (AFR) AF: 0.675 AC: 27954 AN: 41422

American (AMR) AF: 0.365 AC: 5551 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3464

East Asian (EAS) AF: 0.0890 AC: 459 AN: 5158

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4818

European-Finnish (FIN) AF: 0.499 AC: 5258 AN: 10544

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35496 AN: 67916

Other (OTH) AF: 0.506 AC: 1064 AN: 2102

Alfa AF: 0.466 Hom.: 2808

Bravo AF: 0.518

Asia WGS AF: 0.205 AC: 715 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.28
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs313264; hg19: chr2-126102686;