chr10-6072697-C-A

Variant names:

• chr10-6072697-C-A
• rs41295061

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 0.06 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
• Publications: 48 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0174 AC: 723 AN: 41578

American (AMR) AF: 0.0413 AC: 632 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0536 AC: 259 AN: 4830

European-Finnish (FIN) AF: 0.0637 AC: 675 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0914 AC: 6220 AN: 68032

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0511 Hom.: 73

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 10 Pathogenic:1

Sep 01, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

IL2RA-related disorder Benign:1

Feb 22, 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). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.65
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs41295061; hg19: chr10-6114660;