rs11591988

chr10-80130-C-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 0.122 in 152,156 control chromosomes in the GnomAD database, including 2,047 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 (2047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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: 0.122 AC: 18541 AN: 152038 Hom.: 2037 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.122 AC: 18549 AN: 152156 Hom.: 2047 Cov.: 32 AF XY: 0.130 AC XY: 9695 AN XY: 74370

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.110

Alfa AF: 0.116 Hom.: 1611

Bravo AF: 0.126

Asia WGS AF: 0.342 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591988; hg19: chr10-126070;