10-124455610-A-C

Variant names:

• chr10-124455610-A-C
• rs2459210

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 0.581 in 151,878 control chromosomes in the GnomAD database, including 26,934 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 0.58 (26934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88261 AN: 151760 Hom.: 26923 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.581 AC: 88303 AN: 151878 Hom.: 26934 Cov.: 31 AF XY: 0.583 AC XY: 43296 AN XY: 74220

African (AFR) AF: 0.382 AC: 15821 AN: 41412

American (AMR) AF: 0.683 AC: 10422 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1779 AN: 3460

East Asian (EAS) AF: 0.718 AC: 3701 AN: 5156

South Asian (SAS) AF: 0.585 AC: 2811 AN: 4808

European-Finnish (FIN) AF: 0.665 AC: 7005 AN: 10530

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44666 AN: 67938

Other (OTH) AF: 0.581 AC: 1225 AN: 2110

Alfa AF: 0.601 Hom.: 25728

Bravo AF: 0.577

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.85
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2459210; hg19: chr10-126144179;