15-91020599-A-G

Variant names:

• chr15-91020599-A-G
• rs1867225
• NM_018668.5:c.96+1555T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018668.5(VPS33B):​c.96+1555T>C 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 152,046 control chromosomes in the GnomAD database, including 25,986 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 (25986 hom., cov: 32)
• Consequence: VPS33B NM_018668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 6 publications found

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]

ENSG00000284946 (HGNC:):

VPS33B-DT (HGNC:51413): (VPS33B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• 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 rank	MANE	Protein	UniProt
VPS33B	NM_018668.5	c.96+1555T>C		intron_variant	Intron 1 of 22	ENST00000333371.8	NP_061138.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VPS33B	ENST00000333371.8	c.96+1555T>C		intron_variant	Intron 1 of 22	1	NM_018668.5	ENSP00000327650.4
ENSG00000284946	ENST00000643536.1	n.96+1555T>C		intron_variant	Intron 1 of 34			ENSP00000494429.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83625 AN: 151928 Hom.: 25937 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.551 AC: 83738 AN: 152046 Hom.: 25986 Cov.: 32 AF XY: 0.557 AC XY: 41441 AN XY: 74344

African (AFR) AF: 0.777 AC: 32242 AN: 41482

American (AMR) AF: 0.621 AC: 9476 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3466

East Asian (EAS) AF: 0.992 AC: 5141 AN: 5182

South Asian (SAS) AF: 0.701 AC: 3384 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4131 AN: 10560

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26194 AN: 67952

Other (OTH) AF: 0.544 AC: 1149 AN: 2112

Alfa AF: 0.525 Hom.: 3485

Bravo AF: 0.581

Asia WGS AF: 0.850 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1867225; hg19: chr15-91563829;