2-125345109-C-T

Variant names:

• chr2-125345109-C-T
• rs313264

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 0.521 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.521 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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.506

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs313264; hg19: chr2-126102686;