10-125225617-A-T

Variant names:

• chr10-125225617-A-T
• rs2886276

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 0.501 in 152,050 control chromosomes in the GnomAD database, including 22,989 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 0.50 (22989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.501 AC: 76189 AN: 151932 Hom.: 22994 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.501 AC: 76181 AN: 152050 Hom.: 22989 Cov.: 32 AF XY: 0.507 AC XY: 37702 AN XY: 74324

African (AFR) AF: 0.153 AC: 6366 AN: 41494

American (AMR) AF: 0.631 AC: 9624 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2046 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4719 AN: 5176

South Asian (SAS) AF: 0.706 AC: 3403 AN: 4822

European-Finnish (FIN) AF: 0.600 AC: 6335 AN: 10560

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41987 AN: 67968

Other (OTH) AF: 0.547 AC: 1147 AN: 2098

Alfa AF: 0.546 Hom.: 3124

Bravo AF: 0.487

Asia WGS AF: 0.726 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.087
DANN	Benign	0.77
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2886276; hg19: chr10-126914186;