Given REF is incompatible with our hg38 reference sequence (N). Please double check if it's correct.

chrY-1633190-C-A

Position:

• chrY-1633190-C-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/exons	MANE	Protein	UniProt
ASMT_1	NM_001171038.2_1	c.687C>A	p.Tyr229*	stop_gained	7/9
ASMT_1	NM_001416525.1_1	c.603C>A	p.Tyr201*	stop_gained	6/8
ASMT_1	NM_001171039.1_1	c.563-3248C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.687C>A	p.Tyr229*	stop_gained	7/9	1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.603C>A	p.Tyr201*	stop_gained	6/8	1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.563-3248C>A		intron_variant		1		ENSP00000518606.1
ASMT	ENST00000711207.1	n.289-3052C>A		intron_variant		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

Uncertain significance, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Aug 22, 2019

- -

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;