rs4699896
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001164664.2(MAST4):āc.7062A>Gā(p.Thr2354=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 1,551,978 control chromosomes in the GnomAD database, including 7,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.13 ( 2898 hom., cov: 32)
Exomes š: 0.036 ( 4535 hom. )
Consequence
MAST4
NM_001164664.2 synonymous
NM_001164664.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.534
Genes affected
MAST4 (HGNC:19037): (microtubule associated serine/threonine kinase family member 4) This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 5-67166241-A-G is Benign according to our data. Variant chr5-67166241-A-G is described in ClinVar as [Benign]. Clinvar id is 1304156.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.534 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAST4 | NM_001164664.2 | c.7062A>G | p.Thr2354= | synonymous_variant | 29/29 | ENST00000403625.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAST4 | ENST00000403625.7 | c.7062A>G | p.Thr2354= | synonymous_variant | 29/29 | 5 | NM_001164664.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.131 AC: 19888AN: 151862Hom.: 2865 Cov.: 32
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GnomAD3 exomes AF: 0.0918 AC: 14548AN: 158510Hom.: 1621 AF XY: 0.0820 AC XY: 6865AN XY: 83764
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GnomAD4 exome AF: 0.0361 AC: 50479AN: 1400000Hom.: 4535 Cov.: 36 AF XY: 0.0357 AC XY: 24643AN XY: 690598
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GnomAD4 genome ? AF: 0.131 AC: 19982AN: 151978Hom.: 2898 Cov.: 32 AF XY: 0.133 AC XY: 9854AN XY: 74336
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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 | Jul 19, 2021 | - - |
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