rs10512315

chr9-103493040-G-A

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 0.113 in 151,908 control chromosomes in the GnomAD database, including 1,021 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 0.11 (1021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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: 0.113 AC: 17183 AN: 151792 Hom.: 1019 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.113 AC: 17209 AN: 151908 Hom.: 1021 Cov.: 32 AF XY: 0.112 AC XY: 8286 AN XY: 74230

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.132

Alfa AF: 0.115 Hom.: 125

Bravo AF: 0.116

Asia WGS AF: 0.105 AC: 359 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512315; hg19: chr9-106255322;