rs12595616

Positions:

• chr15-91020283-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018668.5(VPS33B):​c.96+1871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,140 control chromosomes in the GnomAD database, including 26,020 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 0.55 (26020 hom., cov: 33)
• Consequence: VPS33B NM_018668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

VPS33B (HGNC:12712): (VPS33B late endosome and lysosome associated) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene is a member of the Sec-1 domain family, and encodes the human ortholog of rat Vps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C vacuolar protein sorting proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Mutations in this gene are associated with arthrogryposis-renal dysfunction-cholestasis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS33B	NM_018668.5	c.96+1871A>G		intron_variant		ENST00000333371.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS33B	ENST00000333371.8	c.96+1871A>G		intron_variant		1	NM_018668.5	P1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83700 AN: 152022 Hom.: 25971 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.551 AC: 83813 AN: 152140 Hom.: 26020 Cov.: 33 AF XY: 0.558 AC XY: 41475 AN XY: 74370

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.545

Alfa AF: 0.496 Hom.: 3523

Bravo AF: 0.581

Asia WGS AF: 0.850 AC: 2950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12595616; hg19: chr15-91563513;