rs765965868

Variant names:

• chr20-58389257-GCCTCGC-G
• rs765965868
• NM_004738.5:c.-192_-187delGCCCTC

Your query was ambiguous. Multiple possible variants found:

• chr20-58389257-GCCTCGC-G
• chr20-58389257-GCCTCGC-GCCTCGCCCTCGC
• chr20-58389257-GCCTCGC-GCCTCGCCCTCGCCCTCGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004738.5(VAPB):​c.-192_-187delGCCCTC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000386 in 518,638 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000039 (0 hom.)
• Consequence: VAPB NM_004738.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34

Genes affected

VAPB (HGNC:12649): (VAMP associated protein B and C) The protein encoded by this gene is a type IV membrane protein found in plasma and intracellular vesicle membranes. The encoded protein is found as a homodimer and as a heterodimer with VAPA. This protein also can interact with VAMP1 and VAMP2 and may be involved in vesicle trafficking. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAPB	NM_004738.5	c.-192_-187delGCCCTC		5_prime_UTR_variant	Exon 1 of 6	ENST00000475243.6	NP_004729.1
VAPB	NM_001195677.2	c.-192_-187delGCCCTC		5_prime_UTR_variant	Exon 1 of 3		NP_001182606.1
VAPB	NR_036633.2	n.40_45delGCCCTC		non_coding_transcript_exon_variant	Exon 1 of 4
VAPB	XR_001754433.3	n.40_45delGCCCTC		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAPB	ENST00000475243	c.-192_-187delGCCCTC		5_prime_UTR_variant	Exon 1 of 6	1	NM_004738.5	ENSP00000417175.1
VAPB	ENST00000395802.7	c.-202_-197delCCTCGC		upstream_gene_variant		1		ENSP00000379147.3
VAPB	ENST00000265619.6	n.-117_-112delCCTCGC		upstream_gene_variant		2
VAPB	ENST00000520497.1	n.-202_-197delCCTCGC		upstream_gene_variant		2		ENSP00000430426.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000863 AC: 1 AN: 115910 Hom.: 0 AF XY: 0.0000156 AC XY: 1 AN XY: 64136

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000486

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000386 AC: 2 AN: 518638 Hom.: 0 AF XY: 0.00000709 AC XY: 2 AN XY: 281988

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000331

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765965868; hg19: chr20-56964313;