rs7937452

Variant names:

• chr11-88493228-C-T
• rs7937452

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 0.0856 in 152,082 control chromosomes in the GnomAD database, including 778 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 0.086 (778 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.0857 AC: 13021 AN: 151964 Hom.: 778 Cov.: 31

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0856 AC: 13021 AN: 152082 Hom.: 778 Cov.: 31 AF XY: 0.0809 AC XY: 6014 AN XY: 74332

African (AFR) AF: 0.0233 AC: 965 AN: 41494

American (AMR) AF: 0.0865 AC: 1322 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0418 AC: 201 AN: 4812

European-Finnish (FIN) AF: 0.0727 AC: 768 AN: 10568

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8994 AN: 67952

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.114 Hom.: 1200

Bravo AF: 0.0832

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7937452; hg19: chr11-88226396; COSMIC: COSV56524485;