chrX-80442907-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152630.5(TENT5D):c.368C>T(p.Pro123Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000043 in 1,209,314 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P123A) has been classified as Uncertain significance.
Frequency
Consequence
NM_152630.5 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 |
---|---|---|---|---|---|---|---|
TENT5D | NM_152630.5 | c.368C>T | p.Pro123Leu | missense_variant | 3/3 | ENST00000308293.6 | |
TENT5D | NM_001170574.2 | c.368C>T | p.Pro123Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5D | ENST00000308293.6 | c.368C>T | p.Pro123Leu | missense_variant | 3/3 | 1 | NM_152630.5 | P1 | |
TENT5D | ENST00000538312.5 | c.368C>T | p.Pro123Leu | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000897 AC: 1AN: 111455Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33731
GnomAD3 exomes AF: 0.0000383 AC: 7AN: 182686Hom.: 0 AF XY: 0.0000889 AC XY: 6AN XY: 67458
GnomAD4 exome AF: 0.0000465 AC: 51AN: 1097859Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 24AN XY: 363409
GnomAD4 genome ? AF: 0.00000897 AC: 1AN: 111455Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33731
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | 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