rs11006074

Variant names:

• chr10-58181691-A-G
• rs11006074

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.105 AC: 4346 AN: 41418

American (AMR) AF: 0.126 AC: 1916 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3472

East Asian (EAS) AF: 0.0937 AC: 483 AN: 5156

South Asian (SAS) AF: 0.144 AC: 692 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1350 AN: 10554

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9801 AN: 67928

Other (OTH) AF: 0.140 AC: 295 AN: 2108

Alfa AF: 0.144 Hom.: 2471

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11006074; hg19: chr10-59941452;