rs41295061

Variant names:

• chr10-6072697-C-A
• rs41295061

Your query was ambiguous. Multiple possible variants found:

• chr10-6072697-C-A
• chr10-6072697-C-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	IL2RA-related disorder (1)
1	-	-	Type 1 diabetes mellitus 10 (1)

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41295061;

hg19: chr10-6114660;