chr2-130152814-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017951.5(SMPD4):c.2225C>T(p.Thr742Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000687 in 1,455,824 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_017951.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMPD4 | NM_017951.5 | c.2225C>T | p.Thr742Ile | missense_variant | 20/20 | ENST00000680298.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMPD4 | ENST00000680298.1 | c.2225C>T | p.Thr742Ile | missense_variant | 20/20 | NM_017951.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243450Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132910
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1455824Hom.: 0 Cov.: 31 AF XY: 0.00000830 AC XY: 6AN XY: 723298
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.2342C>T (p.T781I) alteration is located in exon 20 (coding exon 20) of the SMPD4 gene. This alteration results from a C to T substitution at nucleotide position 2342, causing the threonine (T) at amino acid position 781 to be replaced by an isoleucine (I). 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