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Y-1389254-G-A

Variant names:

• chrY-1389254-G-A
• rs200380474
• ENST00000711212.2:c.585C>T

Variant summary

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

The ENST00000711212.2(SLC25A6):​c.585C>T​(p.Tyr195Tyr) 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: SLC25A6 ENST00000711212.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.543
• Publications: 2 publications found

Genes affected

SLC25A6 (HGNC:10992): (solute carrier family 25 member 6) This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein is implicated in the function of the permability transition pore complex (PTPC), which regulates the release of mitochondrial products that induce apoptosis. The human genome contains several non-transcribed pseudogenes of this gene. [provided by RefSeq, Jun 2013]

SLC25A6 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=5.137).
• BP7: Synonymous conserved (PhyloP=0.543 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711212.2. 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
	SLC25A6_1	NM_001636.4_1		c.585C>T	p.Tyr195Tyr	synonymous	Exon 2 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A6	ENST00000711212.2	TSL:5	c.585C>T	p.Tyr195Tyr	synonymous	Exon 2 of 4	ENSP00000518609.1
	SLC25A6	ENST00000972956.1		c.585C>T	p.Tyr195Tyr	synonymous	Exon 2 of 4	ENSP00000642818.1
	SLC25A6	ENST00000972955.1		c.585C>T	p.Tyr195Tyr	synonymous	Exon 3 of 5	ENSP00000642817.1

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
CADD	Benign	5.1
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs200380474; hg19: chrY-1458147;