rs10792828

Positions:

• chr11-86115755-A-G
• chr11-86115755-A-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 0.0963 in 152,294 control chromosomes in the GnomAD database, including 1,032 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 0.096 (1032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.0963 AC: 14661 AN: 152176 Hom.: 1031 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0963 AC: 14664 AN: 152294 Hom.: 1032 Cov.: 32 AF XY: 0.0991 AC XY: 7381 AN XY: 74464

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0910

Alfa AF: 0.0560 Hom.: 69

Bravo AF: 0.0945

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792828; hg19: chr11-85826797;