rs41295061

Positions:

• chr10-6072697-C-A
• chr10-6072697-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 0.06 in 152,300 control chromosomes in the GnomAD database, including 395 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: 𝑓 0.060 (395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Conflicting classifications of pathogenicity no assertion criteria provided P:1 B:1
• Conservation: PhyloP100: 0.355

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0895 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: 0.0601 AC: 9143 AN: 152182 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0414

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0600 AC: 9143 AN: 152300 Hom.: 395 Cov.: 32 AF XY: 0.0582 AC XY: 4335 AN XY: 74460

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0413

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.0914

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0698 Hom.: 57

Bravo AF: 0.0573

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

TYPE 1 DIABETES MELLITUS, INSULIN-DEPENDENT, 10 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2007

- -

IL2RA-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 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). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41295061; hg19: chr10-6114660;