rs2373962

Variant names:

• chr7-150983889-G-C
• rs2373962

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 0.724 in 152,186 control chromosomes in the GnomAD database, including 41,103 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 0.72 (41103 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.724 AC: 110115 AN: 152068 Hom.: 41038 Cov.: 33

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.724 AC: 110239 AN: 152186 Hom.: 41103 Cov.: 33 AF XY: 0.726 AC XY: 54018 AN XY: 74386

African (AFR) AF: 0.893 AC: 37115 AN: 41554

American (AMR) AF: 0.716 AC: 10936 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4600 AN: 5184

South Asian (SAS) AF: 0.737 AC: 3556 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6930 AN: 10572

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42485 AN: 67976

Other (OTH) AF: 0.689 AC: 1457 AN: 2114

Alfa AF: 0.688 Hom.: 4610

Bravo AF: 0.740

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.59
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs2373962; hg19: chr7-150680977;