X-1636567-TG-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001171038.2(ASMT):c.910+8del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,613,694 control chromosomes in the GnomAD database, including 14,561 homozygotes. There are 106,156 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.15 ( 1827 hom., 11156 hem., cov: 29)
Exomes 𝑓: 0.13 ( 12734 hom. 95000 hem. )
Consequence
ASMT
NM_001171038.2 splice_region, intron
NM_001171038.2 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.602
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant X-1636567-TG-T is Benign according to our data. Variant chrX-1636567-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 3036440.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASMT | NM_001171038.2 | c.910+8del | splice_region_variant, intron_variant | ENST00000381241.9 | |||
ASMT | NM_001171039.1 | c.685+8del | splice_region_variant, intron_variant | ||||
ASMT | NM_001416525.1 | c.826+8del | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.910+8del | splice_region_variant, intron_variant | 1 | NM_001171038.2 | ||||
ASMT | ENST00000381229.9 | c.826+8del | splice_region_variant, intron_variant | 1 | P1 | ||||
ASMT | ENST00000381233.8 | c.685+8del | splice_region_variant, intron_variant | 1 | |||||
ASMT | ENST00000432523.6 | c.163+8del | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.150 AC: 22812AN: 152054Hom.: 1825 Cov.: 29 AF XY: 0.150 AC XY: 11144AN XY: 74256
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GnomAD3 exomes AF: 0.137 AC: 34409AN: 251148Hom.: 2618 AF XY: 0.139 AC XY: 18803AN XY: 135718
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GnomAD4 exome AF: 0.129 AC: 187905AN: 1461522Hom.: 12734 Cov.: 31 AF XY: 0.131 AC XY: 95000AN XY: 727036
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GnomAD4 genome AF: 0.150 AC: 22821AN: 152172Hom.: 1827 Cov.: 29 AF XY: 0.150 AC XY: 11156AN XY: 74384
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ASMT-related disorder Benign:1
Likely benign, criteria provided, single submitter | 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at