Y-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

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.110
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ASMT_1NM_001171038.2_1 linkc.687C>A p.Tyr229* stop_gained 7/9
ASMT_1NM_001416525.1_1 linkc.603C>A p.Tyr201* stop_gained 6/8
ASMT_1NM_001171039.1_1 linkc.563-3248C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ASMTENST00000711210.1 linkc.687C>A p.Tyr229* stop_gained 7/91 ENSP00000518608.1
ASMTENST00000711209.1 linkc.603C>A p.Tyr201* stop_gained 6/81 ENSP00000518607.1
ASMTENST00000711208.1 linkc.563-3248C>A intron_variant 1 ENSP00000518606.1
ASMTENST00000711207.1 linkn.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
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityAug 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs143524297; hg19: chrY-1702083; API