rs9332413

Variant names:

• chr16-23002854-G-A
• rs9332413

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 0.622 in 152,074 control chromosomes in the GnomAD database, including 30,921 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 0.62 (30921 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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: 0.622 AC: 94553 AN: 151958 Hom.: 30903 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.622 AC: 94619 AN: 152074 Hom.: 30921 Cov.: 33 AF XY: 0.620 AC XY: 46049 AN XY: 74316

African (AFR) AF: 0.801 AC: 33228 AN: 41494

American (AMR) AF: 0.462 AC: 7063 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2272 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1234 AN: 5176

South Asian (SAS) AF: 0.747 AC: 3604 AN: 4822

European-Finnish (FIN) AF: 0.567 AC: 5964 AN: 10524

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39121 AN: 67988

Other (OTH) AF: 0.626 AC: 1320 AN: 2108

Alfa AF: 0.578 Hom.: 4624

Bravo AF: 0.616

Asia WGS AF: 0.496 AC: 1729 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	6.4
DANN	Benign	0.72
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9332413; hg19: chr16-23014175;