rs10512315

Variant names:

• chr9-103493040-G-A
• rs10512315

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 0.113 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.109 AC: 4517 AN: 41468

American (AMR) AF: 0.102 AC: 1557 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.135 AC: 699 AN: 5182

South Asian (SAS) AF: 0.111 AC: 535 AN: 4820

European-Finnish (FIN) AF: 0.0618 AC: 649 AN: 10500

Middle Eastern (MID) AF: 0.203 AC: 59 AN: 290

European-Non Finnish (NFE) AF: 0.123 AC: 8344 AN: 67896

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.116 Hom.: 134

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10512315; hg19: chr9-106255322;