rs10813103

chr9-29476690-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 0.0271 in 152,270 control chromosomes in the GnomAD database, including 99 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 0.027 (99 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Benign. Variant got -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 = 0.0764 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: 0.0270 AC: 4106 AN: 152152 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00939

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0271 AC: 4120 AN: 152270 Hom.: 99 Cov.: 32 AF XY: 0.0266 AC XY: 1977 AN XY: 74462

Gnomad4 AFR AF: 0.00967

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0298 Hom.: 7

Bravo AF: 0.0284

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.8
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10813103; hg19: chr9-29476688; COSMIC: COSV69457424;