rs10512240

Variant names:

• chr9-96194206-A-G
• rs10512240

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 0.0346 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00734 AC: 305 AN: 41574

American (AMR) AF: 0.106 AC: 1615 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0234 AC: 81 AN: 3468

East Asian (EAS) AF: 0.117 AC: 606 AN: 5180

South Asian (SAS) AF: 0.0902 AC: 435 AN: 4824

European-Finnish (FIN) AF: 0.0402 AC: 426 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0242 AC: 1645 AN: 68020

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10512240; hg19: chr9-98956488;