2-75041937-T-C

Variant names:

• chr2-75041937-T-C
• rs13012537

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 0.477 in 152,128 control chromosomes in the GnomAD database, including 17,844 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 0.48 (17844 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.477 AC: 72567 AN: 152010 Hom.: 17833 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.477 AC: 72616 AN: 152128 Hom.: 17844 Cov.: 33 AF XY: 0.471 AC XY: 35058 AN XY: 74386

African (AFR) AF: 0.571 AC: 23714 AN: 41506

American (AMR) AF: 0.450 AC: 6875 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5164

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3331 AN: 10582

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30499 AN: 67992

Other (OTH) AF: 0.492 AC: 1038 AN: 2108

Alfa AF: 0.470 Hom.: 33486

Bravo AF: 0.491

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.67
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs13012537; hg19: chr2-75269064;