14-60818634-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002431.4(MNAT1):c.562-88A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,180,028 control chromosomes in the GnomAD database, including 210,641 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 0.48 ( 21155 hom., cov: 32)
Exomes 𝑓: 0.60 ( 189486 hom. )
Consequence
MNAT1
NM_002431.4 intron
NM_002431.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.25
Genes affected
MNAT1 (HGNC:7181): (MNAT1 component of CDK activating kinase) The protein encoded by this gene, along with cyclin H and CDK7, forms the CDK-activating kinase (CAK) enzymatic complex. This complex activates several cyclin-associated kinases and can also associate with TFIIH to activate transcription by RNA polymerase II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNAT1 | NM_002431.4 | c.562-88A>G | intron_variant | ENST00000261245.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNAT1 | ENST00000261245.9 | c.562-88A>G | intron_variant | 1 | NM_002431.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.478 AC: 72617AN: 151840Hom.: 21150 Cov.: 32
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GnomAD4 exome AF: 0.596 AC: 613112AN: 1028070Hom.: 189486 AF XY: 0.596 AC XY: 301427AN XY: 506004
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GnomAD4 genome ? AF: 0.478 AC: 72641AN: 151958Hom.: 21155 Cov.: 32 AF XY: 0.484 AC XY: 35962AN XY: 74272
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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