rs10791740

Positions:

• chr11-104938927-C-T

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 0.328 in 151,872 control chromosomes in the GnomAD database, including 8,548 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 0.33 (8548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.328 AC: 49748 AN: 151754 Hom.: 8536 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.328 AC: 49821 AN: 151872 Hom.: 8548 Cov.: 32 AF XY: 0.329 AC XY: 24445 AN XY: 74242

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.343

Alfa AF: 0.295 Hom.: 8822

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10791740; hg19: chr11-104809654;