rs10513308

Variant names:

• chr9-117699975-C-T
• rs10513308

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0226 in 152,130 control chromosomes in the GnomAD database, including 47 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 0.023 (47 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0226 (3439/152130) while in subpopulation AMR AF = 0.0316 (483/15270). AF 95% confidence interval is 0.0293. There are 47 homozygotes in GnomAd4. There are 1644 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0226 AC: 3430 AN: 152012 Hom.: 47 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.00530

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0298

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

GnomAD4 genome AF: 0.0226 AC: 3439 AN: 152130 Hom.: 47 Cov.: 32 AF XY: 0.0221 AC XY: 1644 AN XY: 74366

African (AFR) AF: 0.0175 AC: 728 AN: 41526

American (AMR) AF: 0.0316 AC: 483 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4816

European-Finnish (FIN) AF: 0.00530 AC: 56 AN: 10566

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1736 AN: 67996

Other (OTH) AF: 0.0294 AC: 62 AN: 2106

Alfa AF: 0.0221 Hom.: 6

Bravo AF: 0.0228

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.24
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs10513308; hg19: chr9-120462253;