chr9-21816574-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002451.4(MTAP):c.121-140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 671,772 control chromosomes in the GnomAD database, including 108,827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.63 ( 31474 hom., cov: 32)
Exomes 𝑓: 0.54 ( 77353 hom. )
Consequence
MTAP
NM_002451.4 intron
NM_002451.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0550
Genes affected
MTAP (HGNC:7413): (methylthioadenosine phosphorylase) This gene encodes an enzyme that plays a major role in polyamine metabolism and is important for the salvage pathway of both adenine and methionine. The encoded enzyme is deficient in many cancers. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 9-21816574-G-A is Benign according to our data. Variant chr9-21816574-G-A is described in ClinVar as [Benign]. Clinvar id is 1230723.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTAP | NM_002451.4 | c.121-140G>A | intron_variant | ENST00000644715.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTAP | ENST00000644715.2 | c.121-140G>A | intron_variant | NM_002451.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.632 AC: 96032AN: 151884Hom.: 31416 Cov.: 32
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GnomAD4 exome AF: 0.540 AC: 280577AN: 519770Hom.: 77353 AF XY: 0.530 AC XY: 145803AN XY: 274892
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GnomAD4 genome ? AF: 0.633 AC: 96153AN: 152002Hom.: 31474 Cov.: 32 AF XY: 0.627 AC XY: 46620AN XY: 74300
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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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at