10-20553102-T-C

Position:

• chr10-20553102-T-C

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 0.125 in 150,708 control chromosomes in the GnomAD database, including 2,086 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 0.13 (2086 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18865 AN: 150596 Hom.: 2081 Cov.: 29

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.125 AC: 18895 AN: 150708 Hom.: 2086 Cov.: 29 AF XY: 0.121 AC XY: 8934 AN XY: 73616

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0752 Hom.: 876

Bravo AF: 0.141

Asia WGS AF: 0.0670 AC: 234 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7081156; hg19: chr10-20842031;