chr10-44360215-A-G

Variant names:

• chr10-44360215-A-G
• rs266105

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 0.839 in 152,140 control chromosomes in the GnomAD database, including 53,756 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (53756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 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: 0.839 AC: 127504 AN: 152022 Hom.: 53717 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.839 AC: 127599 AN: 152140 Hom.: 53756 Cov.: 32 AF XY: 0.840 AC XY: 62462 AN XY: 74382

African (AFR) AF: 0.770 AC: 31948 AN: 41474

American (AMR) AF: 0.802 AC: 12260 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2888 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4433 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3875 AN: 4816

European-Finnish (FIN) AF: 0.931 AC: 9877 AN: 10606

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59369 AN: 68006

Other (OTH) AF: 0.863 AC: 1824 AN: 2114

Alfa AF: 0.860 Hom.: 113933

Bravo AF: 0.827

Asia WGS AF: 0.826 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs266105; hg19: chr10-44855663;