rs830407

chr9-33217268-G-A

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 0.244 in 152,062 control chromosomes in the GnomAD database, including 7,618 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 0.24 (7618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.244 AC: 37102 AN: 151944 Hom.: 7592 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.244 AC: 37177 AN: 152062 Hom.: 7618 Cov.: 32 AF XY: 0.240 AC XY: 17830 AN XY: 74332

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.217

Alfa AF: 0.232 Hom.: 1220

Bravo AF: 0.257

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs830407; hg19: chr9-33217266;