rs7459833

chr8-99123903-A-G

Variant summary

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

The NM_017890.5(VPS13B):c.1206+2458A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,084 control chromosomes in the GnomAD database, including 40,005 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 0.72 (40005 hom., cov: 31)
• Consequence: VPS13B NM_017890.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS13B	NM_017890.5	c.1206+2458A>G		intron_variant		ENST00000358544.7
VPS13B	NM_152564.5	c.1206+2458A>G		intron_variant		ENST00000357162.7
VPS13B	NM_015243.3	c.1206+2458A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS13B	ENST00000357162.7	c.1206+2458A>G		intron_variant		1	NM_152564.5	P1
VPS13B	ENST00000358544.7	c.1206+2458A>G		intron_variant		1	NM_017890.5

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108842 AN: 151966 Hom.: 40001 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.716 AC: 108874 AN: 152084 Hom.: 40005 Cov.: 31 AF XY: 0.714 AC XY: 53090 AN XY: 74332

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.723

Alfa AF: 0.776 Hom.: 45409

Bravo AF: 0.690

Asia WGS AF: 0.681 AC: 2367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.70

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: rs7459833; hg19: chr8-100136131;