18-50721934-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002747.4(MAPK4):c.692-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00811 in 1,613,948 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002747.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK4 | NM_002747.4 | c.692-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000400384.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK4 | ENST00000400384.7 | c.692-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002747.4 | P1 | |||
MAPK4 | ENST00000592595.5 | c.691+6711C>T | intron_variant | 1 | |||||
MAPK4 | ENST00000540640.3 | c.59-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00569 AC: 866AN: 152218Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00606 AC: 1508AN: 248966Hom.: 10 AF XY: 0.00620 AC XY: 837AN XY: 135084
GnomAD4 exome AF: 0.00836 AC: 12216AN: 1461612Hom.: 57 Cov.: 31 AF XY: 0.00806 AC XY: 5864AN XY: 727106
GnomAD4 genome AF: 0.00568 AC: 866AN: 152336Hom.: 6 Cov.: 32 AF XY: 0.00505 AC XY: 376AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | MAPK4: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at