rs10793396

Positions:

• chr11-79811587-T-A
• chr11-79811587-T-C

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 0.43 in 152,014 control chromosomes in the GnomAD database, including 14,725 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 0.43 (14725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65387 AN: 151898 Hom.: 14728 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.430 AC: 65410 AN: 152014 Hom.: 14725 Cov.: 32 AF XY: 0.437 AC XY: 32492 AN XY: 74284

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.453

Alfa AF: 0.445 Hom.: 1893

Bravo AF: 0.420

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10793396; hg19: chr11-79522631;