rs4977746
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000580900.5(MTAP):c.814-10661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,032 control chromosomes in the GnomAD database, including 14,496 homozygotes. 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 0.38 ( 14496 hom., cov: 31)
Consequence
MTAP
ENST00000580900.5 intron
ENST00000580900.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.96
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTAP | NM_001396041.1 | c.814-10661T>C | intron_variant | ||||
MTAP | NM_001396042.1 | c.691-18813T>C | intron_variant | ||||
MTAP | NM_001396043.1 | c.814-18813T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTAP | ENST00000577563.1 | c.148-10661T>C | intron_variant | 1 | |||||
MTAP | ENST00000580900.5 | c.814-10661T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.381 AC: 57809AN: 151912Hom.: 14452 Cov.: 31
GnomAD3 genomes
?
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.381 AC: 57923AN: 152032Hom.: 14496 Cov.: 31 AF XY: 0.385 AC XY: 28573AN XY: 74288
GnomAD4 genome
?
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152032
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31
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28573
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74288
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Asia WGS
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1656
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at