18-79679532-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The XM_047437922.1(CTDP1):āc.131T>Cā(p.Leu44Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 458,636 control chromosomes in the GnomAD database, including 92,442 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
XM_047437922.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTDP1 | XM_047437922.1 | c.131T>C | p.Leu44Pro | missense_variant | 1/13 | XP_047293878.1 | ||
CTDP1 | XM_047437926.1 | c.50T>C | p.Leu17Pro | missense_variant | 1/12 | XP_047293882.1 | ||
CTDP1 | XM_047437924.1 | c.-44+302T>C | intron_variant | XP_047293880.1 | ||||
CTDP1-DT | NR_136643.1 | n.214A>G | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTDP1-DT | ENST00000317008.4 | n.214A>G | non_coding_transcript_exon_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.638 AC: 96749AN: 151756Hom.: 31061 Cov.: 32
GnomAD3 exomes AF: 0.635 AC: 81503AN: 128372Hom.: 26029 AF XY: 0.636 AC XY: 44700AN XY: 70302
GnomAD4 exome AF: 0.630 AC: 193229AN: 306762Hom.: 61348 Cov.: 0 AF XY: 0.636 AC XY: 110939AN XY: 174450
GnomAD4 genome AF: 0.638 AC: 96832AN: 151874Hom.: 31094 Cov.: 32 AF XY: 0.645 AC XY: 47869AN XY: 74254
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at