9-117699343-C-T

Variant names:

• chr9-117699343-C-T
• rs10759930

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 0.311 in 151,956 control chromosomes in the GnomAD database, including 8,896 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 0.31 (8896 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 69 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.311 AC: 47270 AN: 151840 Hom.: 8901 Cov.: 31

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.311 AC: 47271 AN: 151956 Hom.: 8896 Cov.: 31 AF XY: 0.313 AC XY: 23223 AN XY: 74254

African (AFR) AF: 0.0973 AC: 4036 AN: 41492

American (AMR) AF: 0.390 AC: 5945 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3163 AN: 5134

South Asian (SAS) AF: 0.400 AC: 1926 AN: 4818

European-Finnish (FIN) AF: 0.319 AC: 3370 AN: 10568

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26277 AN: 67916

Other (OTH) AF: 0.343 AC: 722 AN: 2102

Alfa AF: 0.355 Hom.: 20503

Bravo AF: 0.310

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10759930; hg19: chr9-120461621;