rs2279103
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004715.5(CTDP1):c.1019C>T(p.Thr340Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,613,250 control chromosomes in the GnomAD database, including 25,155 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. T340T) has been classified as Likely benign.
Frequency
Consequence
NM_004715.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTDP1 | NM_004715.5 | c.1019C>T | p.Thr340Met | missense_variant | 7/13 | ENST00000613122.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTDP1 | ENST00000613122.5 | c.1019C>T | p.Thr340Met | missense_variant | 7/13 | 1 | NM_004715.5 | P1 | |
CTDP1 | ENST00000075430.11 | c.1019C>T | p.Thr340Met | missense_variant | 7/12 | 1 | |||
CTDP1 | ENST00000591598.5 | c.815C>T | p.Thr272Met | missense_variant | 7/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19131AN: 151926Hom.: 1586 Cov.: 32
GnomAD3 exomes AF: 0.136 AC: 33947AN: 250106Hom.: 2806 AF XY: 0.136 AC XY: 18425AN XY: 135306
GnomAD4 exome AF: 0.172 AC: 251721AN: 1461206Hom.: 23570 Cov.: 34 AF XY: 0.169 AC XY: 123002AN XY: 726908
GnomAD4 genome ? AF: 0.126 AC: 19124AN: 152044Hom.: 1585 Cov.: 32 AF XY: 0.122 AC XY: 9098AN XY: 74292
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at