rs10512240

Variant names:

• chr9-96194206-A-G
• rs10512240

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 0.0346 in 152,298 control chromosomes in the GnomAD database, including 210 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 0.035 (210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 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: 0.0345 AC: 5251 AN: 152180 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.00736

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0346 AC: 5273 AN: 152298 Hom.: 210 Cov.: 32 AF XY: 0.0384 AC XY: 2856 AN XY: 74472

Gnomad4 AFR AF: 0.00734

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0242

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0296 Hom.: 17

Bravo AF: 0.0373

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.049
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512240; hg19: chr9-98956488;