rs7931462

chr11-93051037-G-A

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 0.0441 in 152,114 control chromosomes in the GnomAD database, including 256 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 0.044 (256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6698 AN: 151996 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0441 AC: 6712 AN: 152114 Hom.: 256 Cov.: 32 AF XY: 0.0432 AC XY: 3212 AN XY: 74362

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0461

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.0389

Alfa AF: 0.0271 Hom.: 109

Bravo AF: 0.0468

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.65
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7931462; hg19: chr11-92784203;