rs10098153

Positions:

• chr8-99105893-G-A
• chr8-99105893-G-C
• chr8-99105893-G-T

Variant summary

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

The NM_017890.5(VPS13B):​c.580+2773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,020 control chromosomes in the GnomAD database, including 52,302 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 0.83 (52302 hom., cov: 30)
• Consequence: VPS13B NM_017890.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

Genes affected

VPS13B (HGNC:2183): (vacuolar protein sorting 13 homolog B) This gene encodes a potential transmembrane protein that may function in vesicle-mediated transport and sorting of proteins within the cell. This protein may play a role in the development and the function of the eye, hematological system, and central nervous system. Mutations in this gene have been associated with Cohen syndrome. Multiple splice variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VPS13B	NM_017890.5	c.580+2773G>A		intron_variant		ENST00000358544.7	NP_060360.3
VPS13B	NM_152564.5	c.580+2773G>A		intron_variant		ENST00000357162.7	NP_689777.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VPS13B	ENST00000357162.7	c.580+2773G>A		intron_variant		1	NM_152564.5	ENSP00000349685	P1
VPS13B	ENST00000358544.7	c.580+2773G>A		intron_variant		1	NM_017890.5	ENSP00000351346

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125392 AN: 151902 Hom.: 52268 Cov.: 30

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.825 AC: 125479 AN: 152020 Hom.: 52302 Cov.: 30 AF XY: 0.823 AC XY: 61123 AN XY: 74298

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.801

Alfa AF: 0.808 Hom.: 18789

Bravo AF: 0.808

Asia WGS AF: 0.738 AC: 2565 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.25

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: rs10098153; hg19: chr8-100118121;