X-80443692-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_152630.5(TENT5D):c.1153T>A(p.Ser385Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,180,658 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 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.1153T>A | p.Ser385Thr | missense_variant | 3/3 | ENST00000308293.6 | |
TENT5D | NM_001170574.2 | c.1153T>A | p.Ser385Thr | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5D | ENST00000308293.6 | c.1153T>A | p.Ser385Thr | missense_variant | 3/3 | 1 | NM_152630.5 | P1 | |
TENT5D | ENST00000538312.5 | c.1153T>A | p.Ser385Thr | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000893 AC: 1AN: 111941Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34191
GnomAD3 exomes AF: 0.0000477 AC: 8AN: 167743Hom.: 0 AF XY: 0.0000360 AC XY: 2AN XY: 55599
GnomAD4 exome AF: 0.0000384 AC: 41AN: 1068717Hom.: 0 Cov.: 30 AF XY: 0.0000499 AC XY: 17AN XY: 340681
GnomAD4 genome ? AF: 0.00000893 AC: 1AN: 111941Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34191
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.1153T>A (p.S385T) alteration is located in exon 5 (coding exon 1) of the FAM46D gene. This alteration results from a T to A substitution at nucleotide position 1153, causing the serine (S) at amino acid position 385 to be replaced by a threonine (T). 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