19-48607028-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_133498.3(SPACA4):c.50C>T(p.Thr17Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,611,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133498.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPACA4 | NM_133498.3 | c.50C>T | p.Thr17Met | missense_variant | Exon 1 of 1 | ENST00000321762.3 | NP_598005.1 | |
FAM83E | NM_017708.4 | c.758+2848G>A | intron_variant | Intron 5 of 6 | ENST00000263266.4 | NP_060178.2 | ||
FAM83E | XM_024451561.2 | c.758+2848G>A | intron_variant | Intron 5 of 6 | XP_024307329.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPACA4 | ENST00000321762.3 | c.50C>T | p.Thr17Met | missense_variant | Exon 1 of 1 | 6 | NM_133498.3 | ENSP00000312774.1 | ||
FAM83E | ENST00000263266.4 | c.758+2848G>A | intron_variant | Intron 5 of 6 | 1 | NM_017708.4 | ENSP00000263266.2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248834Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134992
GnomAD4 exome AF: 0.000112 AC: 163AN: 1459346Hom.: 0 Cov.: 31 AF XY: 0.0000992 AC XY: 72AN XY: 726136
GnomAD4 genome AF: 0.000138 AC: 21AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.50C>T (p.T17M) alteration is located in exon 1 (coding exon 1) of the SPACA4 gene. This alteration results from a C to T substitution at nucleotide position 50, causing the threonine (T) at amino acid position 17 to be replaced by a methionine (M). 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