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chrY-1629941-T-C

Variant names:

• chrY-1629941-T-C
• rs148855515
• ENST00000711210.1:c.562+2T>C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The ENST00000711210.1(ASMT):​c.562+2T>C variant causes a splice donor, intron change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov:)
• Consequence: ASMT ENST00000711210.1 splice_donor, intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1 B:1
• Conservation: PhyloP100: 5.53

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 Likely_benign. Variant got -1 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=22.1).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASMT_1	NM_001171038.2_1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 8
ASMT_1	NM_001416525.1_1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 7
ASMT_1	NM_001171039.1_1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 8	1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 7	1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.562+2T>C		splice_donor_variant, intron_variant	Intron 5 of 6	1		ENSP00000518606.1
ASMT	ENST00000711207.1	n.288+1908T>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: 0.00245 Hom.: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:1 Benign:1

Jan 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ASMT: BS1, BS2 -

Apr 19, 2022

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs148855515; hg19: chrY-1698834;