rs13283064

Positions:

• chr9-34152466-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.214

Alfa AF: 0.248 Hom.: 3626

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13283064; hg19: chr9-34152464;