2-241030510-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080437.3(SNED1):c.440C>T(p.Thr147Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T147N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080437.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNED1 | ENST00000310397.13 | c.440C>T | p.Thr147Ile | missense_variant | Exon 2 of 32 | 5 | NM_001080437.3 | ENSP00000308893.8 | ||
SNED1 | ENST00000405547.7 | c.440C>T | p.Thr147Ile | missense_variant | Exon 2 of 30 | 5 | ENSP00000386007.3 | |||
SNED1 | ENST00000401884.5 | c.440C>T | p.Thr147Ile | missense_variant | Exon 2 of 27 | 5 | ENSP00000384871.1 | |||
SNED1-AS1 | ENST00000458377.1 | n.140+2991G>A | intron_variant | Intron 2 of 2 | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248650Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135096
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440C>T (p.T147I) alteration is located in exon 2 (coding exon 2) of the SNED1 gene. This alteration results from a C to T substitution at nucleotide position 440, causing the threonine (T) at amino acid position 147 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