X-1636773-C-T

Position:

• chrX-1636773-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001171038.2(ASMT):​c.910+213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,066 control chromosomes in the GnomAD database, including 13,317 homozygotes. There are 31,328 hemizygotes in GnomAD. 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: 𝑓 0.41 (13317 hom., 31328 hem., cov: 33)
• Consequence: ASMT NM_001171038.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASMT	NM_001171038.2	c.910+213C>T		intron_variant		ENST00000381241.9	NP_001164509.1
ASMT	NM_001416525.1	c.826+213C>T		intron_variant			NP_001403454.1
ASMT	NM_001171039.1	c.685+213C>T		intron_variant			NP_001164510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASMT	ENST00000381241.9	c.910+213C>T		intron_variant		1	NM_001171038.2	ENSP00000370639.3
ASMT	ENST00000381229.9	c.826+213C>T		intron_variant		1		ENSP00000370627.4
ASMT	ENST00000381233.8	c.685+213C>T		intron_variant		1		ENSP00000370631.3
ASMT	ENST00000432523.6	c.163+213C>T		intron_variant		2		ENSP00000392053.1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62965 AN: 151948 Hom.: 13295 Cov.: 33 AF XY: 0.421 AC XY: 31252 AN XY: 74178

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.414

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.415 AC: 63036 AN: 152066 Hom.: 13317 Cov.: 33 AF XY: 0.422 AC XY: 31328 AN XY: 74306

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.418

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5949028; hg19: chrX-1755666;