rs9332413

Positions:

• chr16-23002854-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 0.622 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.626

Alfa AF: 0.571 Hom.: 4380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332413; hg19: chr16-23014175;