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chrY-1615250-C-A

Variant names:

• chrY-1615250-C-A
• rs17149149
• ENST00000711206.2:c.51C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000711206.2(ASMT):​c.51C>A​(p.Asn17Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov:)
• Consequence: ASMT ENST00000711206.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1 B:1
• Conservation: PhyloP100: -1.08
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=5.304).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711206.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASMT_1	NM_001171038.2_1		c.51C>A	p.Asn17Lys	missense	Exon 1 of 9
	ASMT_1	NM_001416525.1_1		c.51C>A	p.Asn17Lys	missense	Exon 1 of 8
	ASMT_1	NM_001171039.1_1		c.51C>A	p.Asn17Lys	missense	Exon 1 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASMT	ENST00000711206.2	TSL:2	c.51C>A	p.Asn17Lys	missense	Exon 1 of 9	ENSP00000518605.2
	ASMT	ENST00000972689.1		c.51C>A	p.Asn17Lys	missense	Exon 1 of 8	ENSP00000642747.1
	ASMT	ENST00000972690.1		c.51C>A	p.Asn17Lys	missense	Exon 1 of 7	ENSP00000642748.1

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: 0.000796 Hom.: 2

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	ASMT-related disorder (1)
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.65
CADD	Benign	5.3
PhyloP100		-1.1
PromoterAI		-0.036	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17149149; hg19: chrY-1684143;