X-13662822-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001297563.2(TCEANC):c.314C>T(p.Pro105Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00058 in 1,209,817 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 207 hemizygotes in GnomAD. 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 Likely benign (★).
Frequency
Consequence
NM_001297563.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCEANC | NM_001297563.2 | c.314C>T | p.Pro105Leu | missense_variant | Exon 5 of 5 | ENST00000696128.1 | NP_001284492.1 | |
TCEANC | NM_152634.4 | c.404C>T | p.Pro135Leu | missense_variant | Exon 4 of 4 | NP_689847.2 | ||
TCEANC | NM_001297564.2 | c.314C>T | p.Pro105Leu | missense_variant | Exon 3 of 3 | NP_001284493.1 | ||
TCEANC | XM_017029316.2 | c.404C>T | p.Pro135Leu | missense_variant | Exon 4 of 4 | XP_016884805.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000258 AC: 29AN: 112286Hom.: 0 Cov.: 23 AF XY: 0.000290 AC XY: 10AN XY: 34442
GnomAD3 exomes AF: 0.000268 AC: 48AN: 179342Hom.: 0 AF XY: 0.000198 AC XY: 13AN XY: 65520
GnomAD4 exome AF: 0.000613 AC: 673AN: 1097531Hom.: 0 Cov.: 31 AF XY: 0.000543 AC XY: 197AN XY: 362973
GnomAD4 genome AF: 0.000258 AC: 29AN: 112286Hom.: 0 Cov.: 23 AF XY: 0.000290 AC XY: 10AN XY: 34442
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at