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Y-1632709-T-C

Variant names:

• chrY-1632709-T-C
• rs6588809
• ENST00000711206.2:c.568T>C

Variant summary

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

The ENST00000711206.2(ASMT):​c.568T>C​(p.Trp190Arg) variant causes a missense 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: ASMT ENST00000711206.2 missense
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0970
• Publications: 2 publications found

Genes affected

ASMT (HGNC:750): (acetylserotonin O-methyltransferase) This gene belongs to the methyltransferase superfamily, and is located in the pseudoautosomal region (PAR) at the end of the short arms of the X and Y chromosomes. The encoded enzyme catalyzes the final reaction in the synthesis of melatonin, and is abundant in the pineal gland. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Jan 2010]

ASMT (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=8.769).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711206.2. 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
	ASMT_1	NM_001171038.2_1		c.568T>C	p.Trp190Arg	missense	Exon 6 of 9
	ASMT_1	NM_001416525.1_1		c.563-441T>C		intron	N/A
	ASMT_1	NM_001171039.1_1		c.562+2770T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASMT	ENST00000711206.2	TSL:2	c.568T>C	p.Trp190Arg	missense	Exon 6 of 9	ENSP00000518605.2
	ASMT	ENST00000972689.1		c.563-441T>C		intron	N/A	ENSP00000642747.1
	ASMT	ENST00000972690.1		c.562+2770T>C		intron	N/A	ENSP00000642748.1

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: 0.417 Hom.: 2360

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
CADD	Benign	8.8
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs6588809; hg19: chrY-1701602;