15-51692166-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013243.4(SCG3):c.698T>A(p.Met233Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,607,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. M233V) has been classified as Likely benign.
Frequency
Consequence
NM_013243.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCG3 | NM_013243.4 | c.698T>A | p.Met233Lys | missense_variant | 7/12 | ENST00000220478.8 | |
SCG3 | NM_001165257.2 | c.2T>A | p.Met1? | start_lost | 6/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCG3 | ENST00000220478.8 | c.698T>A | p.Met233Lys | missense_variant | 7/12 | 1 | NM_013243.4 | P1 | |
SCG3 | ENST00000542355.6 | c.2T>A | p.Met1? | start_lost | 6/11 | 2 | |||
SCG3 | ENST00000558709.1 | c.2T>A | p.Met1? | start_lost | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000527 AC: 13AN: 246448Hom.: 0 AF XY: 0.0000450 AC XY: 6AN XY: 133210
GnomAD4 exome AF: 0.0000234 AC: 34AN: 1455124Hom.: 0 Cov.: 30 AF XY: 0.0000221 AC XY: 16AN XY: 723544
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.698T>A (p.M233K) alteration is located in exon 7 (coding exon 7) of the SCG3 gene. This alteration results from a T to A substitution at nucleotide position 698, causing the methionine (M) at amino acid position 233 to be replaced by a lysine (K). 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