rs10502058

chr11-105603360-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 0.122 in 152,236 control chromosomes in the GnomAD database, including 1,256 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 0.12 (1256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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: 0.121 AC: 18481 AN: 152118 Hom.: 1246 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.122 AC: 18525 AN: 152236 Hom.: 1256 Cov.: 32 AF XY: 0.122 AC XY: 9045 AN XY: 74438

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.130

Alfa AF: 0.112 Hom.: 1350

Bravo AF: 0.125

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.024
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502058; hg19: chr11-105474087;