rs10792830

chr11-86127766-G-Achr11-86127766-G-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 0.509 in 152,002 control chromosomes in the GnomAD database, including 20,602 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 (20602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.509 AC: 77364 AN: 151884 Hom.: 20586 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.509 AC: 77433 AN: 152002 Hom.: 20602 Cov.: 32 AF XY: 0.503 AC XY: 37411 AN XY: 74306

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.493

Alfa AF: 0.446 Hom.: 32434

Bravo AF: 0.528

Asia WGS AF: 0.545 AC: 1889 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	16
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792830; hg19: chr11-85838808; COSMIC: COSV52478671;