rs13283064

Variant names:

• chr9-34152466-C-T
• rs13283064

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 0.203 in 152,074 control chromosomes in the GnomAD database, including 3,630 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 0.20 (3630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.203 AC: 30886 AN: 151956 Hom.: 3628 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.203 AC: 30892 AN: 152074 Hom.: 3630 Cov.: 32 AF XY: 0.202 AC XY: 15043 AN XY: 74340

African (AFR) AF: 0.110 AC: 4561 AN: 41496

American (AMR) AF: 0.205 AC: 3127 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 664 AN: 3466

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5184

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10572

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18157 AN: 67952

Other (OTH) AF: 0.214 AC: 453 AN: 2116

Alfa AF: 0.246 Hom.: 4213

Bravo AF: 0.195

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs13283064; hg19: chr9-34152464;