chrX-80442672-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_152630.5(TENT5D):c.133C>T(p.His45Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000678 in 1,209,162 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. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152630.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5D | NM_152630.5 | c.133C>T | p.His45Tyr | missense_variant | 3/3 | ENST00000308293.6 | |
TENT5D | NM_001170574.2 | c.133C>T | p.His45Tyr | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5D | ENST00000308293.6 | c.133C>T | p.His45Tyr | missense_variant | 3/3 | 1 | NM_152630.5 | P1 | |
TENT5D | ENST00000538312.5 | c.133C>T | p.His45Tyr | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000313 AC: 35AN: 111693Hom.: 0 Cov.: 23 AF XY: 0.000353 AC XY: 12AN XY: 33965
GnomAD3 exomes AF: 0.0000931 AC: 17AN: 182625Hom.: 0 AF XY: 0.0000742 AC XY: 5AN XY: 67393
GnomAD4 exome AF: 0.0000428 AC: 47AN: 1097420Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 12AN XY: 363090
GnomAD4 genome ? AF: 0.000313 AC: 35AN: 111742Hom.: 0 Cov.: 23 AF XY: 0.000353 AC XY: 12AN XY: 34024
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2023 | The c.133C>T (p.H45Y) alteration is located in exon 5 (coding exon 1) of the FAM46D gene. This alteration results from a C to T substitution at nucleotide position 133, causing the histidine (H) at amino acid position 45 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at