rs11591710

chr10-103927874-A-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 0.161 in 152,136 control chromosomes in the GnomAD database, including 2,352 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 0.16 (2352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.161 AC: 24412 AN: 152018 Hom.: 2336 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.161 AC: 24468 AN: 152136 Hom.: 2352 Cov.: 32 AF XY: 0.156 AC XY: 11632 AN XY: 74390

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0891

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.158

Alfa AF: 0.149 Hom.: 231

Bravo AF: 0.164

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591710; hg19: chr10-105687632;