chr10-53164852-T-C

Variant names:

• chr10-53164852-T-C
• rs1903942

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 0.833 in 151,930 control chromosomes in the GnomAD database, including 53,014 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 0.83 (53014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.833 AC: 126424 AN: 151812 Hom.: 52974 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.833 AC: 126524 AN: 151930 Hom.: 53014 Cov.: 32 AF XY: 0.827 AC XY: 61389 AN XY: 74224

African (AFR) AF: 0.877 AC: 36370 AN: 41482

American (AMR) AF: 0.714 AC: 10854 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2796 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3346 AN: 5122

South Asian (SAS) AF: 0.826 AC: 3978 AN: 4816

European-Finnish (FIN) AF: 0.830 AC: 8763 AN: 10562

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57615 AN: 67950

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.839 Hom.: 229510

Bravo AF: 0.827

Asia WGS AF: 0.752 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.52
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1903942; hg19: chr10-54924612;