Y-1636567-TG-T

Position:

• chrY-1636567-TG-T

Variant summary

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

The ENST00000711210.1(ASMT):​c.910+8delN variant causes a splice region, intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., N/A hem., cov:)
  • Exomes 𝑓: N/A (N/A hom. N/A hem.)
• Consequence: ASMT ENST00000711210.1 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: No conservation score assigned

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_1 (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.910+8delN		splice_region_variant, intron_variant
ASMT_1	NM_001416525.1_1	c.826+8delN		splice_region_variant, intron_variant
ASMT_1	NM_001171039.1_1	c.685+8delN		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.910+8delN		splice_region_variant, intron_variant		1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.826+8delN		splice_region_variant, intron_variant		1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.685+8delN		splice_region_variant, intron_variant		1		ENSP00000518606.1
ASMT	ENST00000711206.1	c.163+8delN		splice_region_variant, intron_variant		2		ENSP00000518605.1

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.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

ASMT-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 2021

This variant is classified as likely 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

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrY-1705460;