chr11-93051037-G-A

Variant names:

• chr11-93051037-G-A
• rs7931462

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;