rs11594656

Variant names:

• chr10-6080046-T-A
• rs11594656

Variant summary

Our verdict is Benign. The variant received -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 (no stars).

• Frequency: Genomes: 𝑓 0.18 (3369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Likely benign no assertion criteria provided B:1 O:1
• Conservation: PhyloP100: 0.206
• Publications: 89 publications found

ACMG classification

Our verdict: Benign. The variant received -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. ClinVar VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0513 AC: 2129 AN: 41490

American (AMR) AF: 0.228 AC: 3484 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3472

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5180

South Asian (SAS) AF: 0.187 AC: 902 AN: 4814

European-Finnish (FIN) AF: 0.169 AC: 1785 AN: 10562

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17169 AN: 67982

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.222 Hom.: 619

Bravo AF: 0.182

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

IL2RA-related disorder Benign:1

Feb 27, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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 Other:1

Apr 17, 2025

OMIM

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.4
DANN	Benign	0.77
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11594656; hg19: chr10-6122009;