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chrY-1623310-A-G

Position:

• chrY-1623310-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The ENST00000711210.1(ASMT):​c.241A>G​(p.Lys81Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: not found (cov:)
• Consequence: ASMT ENST00000711210.1 missense
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.168

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.028).
• BP6: Variant Y-1623310-A-G is Benign according to our data. Variant chrY-1623310-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 599440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASMT_1	NM_001171038.2_1	c.241A>G	p.Lys81Glu	missense_variant	2/9
ASMT_1	NM_001416525.1_1	c.241A>G	p.Lys81Glu	missense_variant	2/8
ASMT_1	NM_001171039.1_1	c.241A>G	p.Lys81Glu	missense_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000711210.1	c.241A>G	p.Lys81Glu	missense_variant	2/9	1		ENSP00000518608.1
ASMT	ENST00000711209.1	c.241A>G	p.Lys81Glu	missense_variant	2/8	1		ENSP00000518607.1
ASMT	ENST00000711208.1	c.241A>G	p.Lys81Glu	missense_variant	2/7	1		ENSP00000518606.1

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: 0.000309 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital

Sep 05, 2017

BS3, BP4; This alteration was found through a well-established in vitro or in vivo functional study to shown no damaging effect on protein function or splicing, and is predicted to be tolerated by multiple functional prediction tools. -

not provided Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
CADD	Benign	0.028

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117343570; hg19: chrY-1692203;