rs10790711

Variant names:

• chr11-124844793-T-C
• rs10790711

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 0.529 in 152,102 control chromosomes in the GnomAD database, including 21,523 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 0.53 (21523 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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: 0.529 AC: 80349 AN: 151984 Hom.: 21484 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.529 AC: 80444 AN: 152102 Hom.: 21523 Cov.: 33 AF XY: 0.530 AC XY: 39436 AN XY: 74340

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.520

Alfa AF: 0.533 Hom.: 3654

Bravo AF: 0.534

Asia WGS AF: 0.416 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10790711; hg19: chr11-124714689;