rs10510039

Variant names:

• chr10-117961208-A-G
• rs10510039

Your query was ambiguous. Multiple possible variants found:

• chr10-117961208-A-G
• chr10-117961208-A-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 0.0642 in 118,148 control chromosomes in the GnomAD database, including 541 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 0.064 (541 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 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: 0.0641 AC: 7569 AN: 118084 Hom.: 539 Cov.: 24

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00358

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.0405

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.00446

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0642 AC: 7588 AN: 118148 Hom.: 541 Cov.: 24 AF XY: 0.0682 AC XY: 3685 AN XY: 54022

African (AFR) AF: 0.173 AC: 5417 AN: 31224

American (AMR) AF: 0.0866 AC: 713 AN: 8230

Ashkenazi Jewish (ASJ) AF: 0.0405 AC: 132 AN: 3260

East Asian (EAS) AF: 0.191 AC: 754 AN: 3950

South Asian (SAS) AF: 0.0158 AC: 60 AN: 3804

European-Finnish (FIN) AF: 0.0277 AC: 111 AN: 4002

Middle Eastern (MID) AF: 0.145 AC: 18 AN: 124

European-Non Finnish (NFE) AF: 0.00446 AC: 273 AN: 61148

Other (OTH) AF: 0.0682 AC: 107 AN: 1568

Alfa AF: 0.0318 Hom.: 135

Bravo AF: 0.0667

Asia WGS AF: 0.0910 AC: 314 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.68
PhyloP100		1.1

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: rs10510039;

hg19: chr10-119720719;

COSMIC: COSV68860882;