rs10513308

Positions:

• chr9-117699975-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0226 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

Gnomad4 AFR AF: 0.0175

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.00530

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0231 Hom.: 3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513308; hg19: chr9-120462253;