10-29879770-C-T

Variant names:

• chr10-29879770-C-T
• rs2202

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 0.731 in 152,106 control chromosomes in the GnomAD database, including 41,250 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 0.73 (41250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111120 AN: 151988 Hom.: 41192 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.731 AC: 111237 AN: 152106 Hom.: 41250 Cov.: 32 AF XY: 0.727 AC XY: 54017 AN XY: 74352

African (AFR) AF: 0.865 AC: 35939 AN: 41526

American (AMR) AF: 0.690 AC: 10542 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2443 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4048 AN: 5176

South Asian (SAS) AF: 0.678 AC: 3258 AN: 4804

European-Finnish (FIN) AF: 0.660 AC: 6973 AN: 10562

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45593 AN: 67976

Other (OTH) AF: 0.719 AC: 1518 AN: 2110

Alfa AF: 0.703 Hom.: 14467

Bravo AF: 0.740

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.33
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs2202; hg19: chr10-30168699;