13-113242969-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001008895.4(CUL4A):c.1037C>G(p.Thr346Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000549 in 1,601,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_001008895.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUL4A | NM_001008895.4 | c.1037C>G | p.Thr346Ser | missense_variant, splice_region_variant | 11/20 | ENST00000375440.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUL4A | ENST00000375440.9 | c.1037C>G | p.Thr346Ser | missense_variant, splice_region_variant | 11/20 | 1 | NM_001008895.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 249902Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135016
GnomAD4 exome AF: 0.0000573 AC: 83AN: 1449394Hom.: 0 Cov.: 30 AF XY: 0.0000780 AC XY: 56AN XY: 718298
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CUL4A: PM2:Supporting, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at