rs4798680
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395333.1(MTCL1):c.1437+10232G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,038 control chromosomes in the GnomAD database, including 9,093 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 0.33 ( 9093 hom., cov: 32)
Consequence
MTCL1
NM_001395333.1 intron
NM_001395333.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.06
Genes affected
MTCL1 (HGNC:29121): (microtubule crosslinking factor 1) Enables microtubule binding activity. Predicted to be involved in establishment or maintenance of epithelial cell apical/basal polarity; microtubule bundle formation; and positive regulation of protein targeting to membrane. Located in midbody and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTCL1 | NM_001395333.1 | c.1437+10232G>A | intron_variant | ENST00000695636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCL1 | ENST00000695636.1 | c.1437+10232G>A | intron_variant | NM_001395333.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49703AN: 151920Hom.: 9087 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.327 AC: 49716AN: 152038Hom.: 9093 Cov.: 32 AF XY: 0.329 AC XY: 24453AN XY: 74322
GnomAD4 genome
?
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49716
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32
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24453
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74322
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1717
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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