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chrY-1633190-C-A

Variant names:

• chrY-1633190-C-A
• rs143524297
• ENST00000711210.1:c.687C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000711210.1(ASMT):​c.687C>A​(p.Tyr229*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov:)
• Consequence: ASMT ENST00000711210.1 stop_gained
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.110

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASMT_1	NM_001171038.2_1	c.687C>A	p.Tyr229*	stop_gained	Exon 7 of 9
ASMT_1	NM_001416525.1_1	c.603C>A	p.Tyr201*	stop_gained	Exon 6 of 8
ASMT_1	NM_001171039.1_1	c.563-3248C>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.687C>A	p.Tyr229*	stop_gained	Exon 7 of 9	1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.603C>A	p.Tyr201*	stop_gained	Exon 6 of 8	1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.563-3248C>A		intron_variant	Intron 5 of 6	1		ENSP00000518606.1
ASMT	ENST00000711207.1	n.289-3052C>A		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: 0.0000979 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Aug 22, 2019

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Uncertain	24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs143524297; hg19: chrY-1702083;