10-29879770-C-T

Variant names:

• chr10-29879770-C-T
• rs2202

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.719

Alfa AF: 0.701 Hom.: 11345

Bravo AF: 0.740

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202; hg19: chr10-30168699;