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Y-57126304-C-T

Variant names:

• chrY-57126304-C-T
• rs138653672
• ENST00000711265.2:c.585C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The ENST00000711265.2(VAMP7):​c.585C>T​(p.Ile195Ile) variant causes a synonymous 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 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.68
• Publications: 3 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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=15.7).
• BP7: Synonymous conserved (PhyloP=-1.68 with no splicing effect.

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.517C>T	p.Arg173Cys	missense	Exon 6 of 7
	VAMP7_1	NM_005638.6_1		c.585C>T	p.Ile195Ile	synonymous	Exon 7 of 8
	VAMP7_1	NM_001145149.3_1		c.462C>T	p.Ile154Ile	synonymous	Exon 6 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAMP7	ENST00000711265.2	TSL:1	c.585C>T	p.Ile195Ile	synonymous	Exon 7 of 8	ENSP00000518619.2
	VAMP7	ENST00000972675.1		c.517C>T	p.Arg173Cys	missense	Exon 6 of 7	ENSP00000642734.1
	VAMP7	ENST00000973017.1		c.603C>T	p.Ile201Ile	synonymous	Exon 8 of 9	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: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
CADD	Benign	16
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs138653672; hg19: chrY-59272454;