rs11006074

Variant names:

• chr10-58181691-A-G
• rs11006074

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 0.13 in 151,908 control chromosomes in the GnomAD database, including 1,290 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 0.13 (1290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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: 0.130 AC: 19780 AN: 151790 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.130 AC: 19806 AN: 151908 Hom.: 1290 Cov.: 32 AF XY: 0.129 AC XY: 9571 AN XY: 74258

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0937

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.140

Alfa AF: 0.145 Hom.: 1979

Bravo AF: 0.129

Asia WGS AF: 0.126 AC: 437 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11006074; hg19: chr10-59941452;