2-112926298-C-T

Variant names:

• chr2-112926298-C-T
• rs10864907

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 0.383 in 152,078 control chromosomes in the GnomAD database, including 13,136 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 0.38 (13136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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: 0.384 AC: 58279 AN: 151960 Hom.: 13131 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.383 AC: 58300 AN: 152078 Hom.: 13136 Cov.: 32 AF XY: 0.388 AC XY: 28855 AN XY: 74336

African (AFR) AF: 0.138 AC: 5732 AN: 41502

American (AMR) AF: 0.528 AC: 8067 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1661 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2490 AN: 4828

European-Finnish (FIN) AF: 0.501 AC: 5289 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32101 AN: 67964

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.434 Hom.: 21449

Bravo AF: 0.373

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10864907; hg19: chr2-113683875; COSMIC: COSV60092765;