rs11594656

Positions:

• chr10-6080046-T-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.183 in 152,076 control chromosomes in the GnomAD database, including 3,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign,protective (no stars).

• Frequency: Genomes: 𝑓 0.18 (3369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Likely benign; protective no assertion criteria provided B:2
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 10-6080046-T-A is Benign according to our data. Variant chr10-6080046-T-A is described in ClinVar as [Likely_benign, protective]. Clinvar id is 14670.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27786 AN: 151958 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.183 AC: 27791 AN: 152076 Hom.: 3369 Cov.: 32 AF XY: 0.178 AC XY: 13251 AN XY: 74350

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.244

Alfa AF: 0.222 Hom.: 619

Bravo AF: 0.182

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Significance: Likely benign; protective

Submissions summary: Benign:2

Revision: no assertion criteria provided

Submissions by phenotype

IL2RA-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 27, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Type 1 diabetes mellitus 10 Benign:1

protective, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11594656; hg19: chr10-6122009;