X-21967073-TTTATTTATTTATTTATTTAC-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_004595.5(SMS):c.50-108_50-89del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 349,806 control chromosomes in the GnomAD database, including 6,045 homozygotes. There are 19,522 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 928 hom., 3730 hem., cov: 16)
Exomes 𝑓: 0.25 ( 5117 hom. 15792 hem. )
Consequence
SMS
NM_004595.5 intron
NM_004595.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.43
Genes affected
SMS (HGNC:11123): (spermine synthase) This gene encodes a protein belonging to the spermidine/spermin synthase family and catalyzes the production of spermine from spermidine. Pseudogenes of this gene are located on chromosomes 1, 5, 6 and X. Mutations in this gene cause an X-linked intellectual disability called Snyder-Robinson Syndrome (SRS). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant X-21967073-TTTATTTATTTATTTATTTAC-T is Benign according to our data. Variant chrX-21967073-TTTATTTATTTATTTATTTAC-T is described in ClinVar as [Benign]. Clinvar id is 1180100.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMS | NM_004595.5 | c.50-108_50-89del | intron_variant | ENST00000404933.7 | NP_004586.2 | |||
SMS | NM_001258423.2 | c.50-108_50-89del | intron_variant | NP_001245352.1 | ||||
SMS | XM_005274582.3 | c.-53-108_-53-89del | intron_variant | XP_005274639.1 | ||||
SMS | XM_011545568.3 | c.-53-108_-53-89del | intron_variant | XP_011543870.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMS | ENST00000404933.7 | c.50-108_50-89del | intron_variant | 1 | NM_004595.5 | ENSP00000385746 | P1 | |||
SMS | ENST00000379404.5 | c.50-108_50-89del | intron_variant | 3 | ENSP00000368714 | |||||
SMS | ENST00000457085.2 | c.395-108_395-89del | intron_variant | 5 | ENSP00000407366 | |||||
SMS | ENST00000478094.1 | n.97-108_97-89del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 14969AN: 90846Hom.: 928 Cov.: 16 AF XY: 0.169 AC XY: 3728AN XY: 22078
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GnomAD4 exome AF: 0.249 AC: 64612AN: 258969Hom.: 5117 AF XY: 0.331 AC XY: 15792AN XY: 47683
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GnomAD4 genome AF: 0.165 AC: 14963AN: 90837Hom.: 928 Cov.: 16 AF XY: 0.169 AC XY: 3730AN XY: 22095
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at