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chrY-1632709-T-C

Variant names:

• chrY-1632709-T-C
• rs6588809
• ENST00000711210.1:c.568T>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP6

The ENST00000711210.1(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. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: not found (cov:)
• Consequence: ASMT ENST00000711210.1 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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=8.769).
• BP6: Variant Y-1632709-T-C is Benign according to our data. Variant chrY-1632709-T-C is described in ClinVar as [Benign]. Clinvar id is 3036492.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASMT_1	NM_001171038.2_1	c.568T>C	p.Trp190Arg	missense_variant	Exon 6 of 9
ASMT_1	NM_001416525.1_1	c.563-441T>C		intron_variant	Intron 5 of 7
ASMT_1	NM_001171039.1_1	c.562+2770T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.568T>C	p.Trp190Arg	missense_variant	Exon 6 of 9	1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.563-441T>C		intron_variant	Intron 5 of 7	1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.562+2770T>C		intron_variant	Intron 5 of 6	1		ENSP00000518606.1
ASMT	ENST00000711207.1	n.289-3533T>C		intron_variant	Intron 1 of 1	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

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

ASMT-related disorder Benign:1

Feb 22, 2023

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
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;