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ENST00000711264.1:c.527-10G>C

Variant names:

• chrY-57128393-G-C
• rs5940625
• ENST00000711265.2:c.595-10G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000711265.2(VAMP7):​c.595-10G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov:)
• Consequence: VAMP7 ENST00000711265.2 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.269
• Publications: 1 publications found

Genes affected

VAMP7 (HGNC:11486): (vesicle associated membrane protein 7) This gene encodes a transmembrane protein that is a member of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family. The encoded protein localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]

VAMP7 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=4.685).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711265.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAMP7_1	NM_001185183.2_1		c.527-10G>C		intron	N/A
	VAMP7_1	NM_005638.6_1		c.595-10G>C		intron	N/A
	VAMP7_1	NM_001145149.3_1		c.472-10G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAMP7	ENST00000711265.2	TSL:1	c.595-10G>C		intron	N/A	ENSP00000518619.2
	VAMP7	ENST00000972675.1		c.527-10G>C		intron	N/A	ENSP00000642734.1
	VAMP7	ENST00000973017.1		c.613-10G>C		intron	N/A	ENSP00000642879.1

Frequencies

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

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

Alfa AF: 0.254 Hom.: 910

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	VAMP7-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.7
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs5940625; hg19: chrY-59274543;