15-43403732-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_014444.5(TUBGCP4):c.1781C>T(p.Ser594Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000121 in 1,613,408 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S594S) has been classified as Likely benign.
Frequency
Consequence
NM_014444.5 missense
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 |
---|---|---|---|---|---|---|---|
TUBGCP4 | NM_014444.5 | c.1781C>T | p.Ser594Leu | missense_variant | 16/18 | ENST00000564079.6 | |
TP53BP1 | NM_001141980.3 | c.*3651G>A | 3_prime_UTR_variant | 28/28 | ENST00000382044.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP4 | ENST00000564079.6 | c.1781C>T | p.Ser594Leu | missense_variant | 16/18 | 1 | NM_014444.5 | A1 | |
TP53BP1 | ENST00000382044.9 | c.*3651G>A | 3_prime_UTR_variant | 28/28 | 1 | NM_001141980.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000710 AC: 108AN: 152108Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000177 AC: 44AN: 249120Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135160
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461182Hom.: 0 Cov.: 30 AF XY: 0.0000523 AC XY: 38AN XY: 726902
GnomAD4 genome AF: 0.000709 AC: 108AN: 152226Hom.: 1 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Microcephaly and chorioretinopathy 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at