11-92965261-C-G

Variant names:

• chr11-92965261-C-G
• rs10830962

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 0.506 in 152,026 control chromosomes in the GnomAD database, including 21,683 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 0.51 (21683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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: 0.505 AC: 76775 AN: 151908 Hom.: 21640 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.506 AC: 76870 AN: 152026 Hom.: 21683 Cov.: 32 AF XY: 0.502 AC XY: 37314 AN XY: 74284

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.489

Alfa AF: 0.392 Hom.: 6228

Bravo AF: 0.515

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10830962; hg19: chr11-92698427;