NM_006659.4:c.2700C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_006659.4(TUBGCP2):c.2700C>T(p.Thr900Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000398 in 1,558,660 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 (no stars).
Frequency
Consequence
NM_006659.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBGCP2 | NM_006659.4 | c.2700C>T | p.Thr900Thr | synonymous_variant | Exon 18 of 18 | ENST00000252936.8 | NP_006650.1 | |
TUBGCP2 | NM_001256617.2 | c.2784C>T | p.Thr928Thr | synonymous_variant | Exon 19 of 19 | NP_001243546.1 | ||
TUBGCP2 | NM_001256618.2 | c.2310C>T | p.Thr770Thr | synonymous_variant | Exon 17 of 17 | NP_001243547.1 | ||
TUBGCP2 | NR_046330.2 | n.3420C>T | non_coding_transcript_exon_variant | Exon 18 of 18 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000183 AC: 30AN: 164302Hom.: 1 AF XY: 0.000169 AC XY: 15AN XY: 88656
GnomAD4 exome AF: 0.0000391 AC: 55AN: 1406412Hom.: 1 Cov.: 31 AF XY: 0.0000403 AC XY: 28AN XY: 694794
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74382
ClinVar
Submissions by phenotype
TUBGCP2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at