10-119618738-T-C

Variant names:

• chr10-119618738-T-C
• rs84086

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 0.638 in 151,844 control chromosomes in the GnomAD database, including 31,893 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 0.64 (31893 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.99
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.637 AC: 96720 AN: 151726 Hom.: 31828 Cov.: 30

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.638 AC: 96843 AN: 151844 Hom.: 31893 Cov.: 30 AF XY: 0.636 AC XY: 47188 AN XY: 74172

African (AFR) AF: 0.792 AC: 32799 AN: 41420

American (AMR) AF: 0.629 AC: 9585 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1704 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4570 AN: 5148

South Asian (SAS) AF: 0.678 AC: 3257 AN: 4806

European-Finnish (FIN) AF: 0.520 AC: 5467 AN: 10516

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37322 AN: 67948

Other (OTH) AF: 0.640 AC: 1346 AN: 2104

Alfa AF: 0.577 Hom.: 32634

Bravo AF: 0.652

Asia WGS AF: 0.778 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.033
DANN	Benign	0.28
PhyloP100		-6.0

Splicing

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

Other links and lift over

dbSNP: rs84086; hg19: chr10-121378250;