2-223598336-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003469.5(SCG2):āc.947G>Cā(p.Arg316Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003469.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCG2 | NM_003469.5 | c.947G>C | p.Arg316Thr | missense_variant | 2/2 | ENST00000305409.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCG2 | ENST00000305409.3 | c.947G>C | p.Arg316Thr | missense_variant | 2/2 | 1 | NM_003469.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251152Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135784
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727178
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2021 | The c.947G>C (p.R316T) alteration is located in exon 2 (coding exon 1) of the SCG2 gene. This alteration results from a G to C substitution at nucleotide position 947, causing the arginine (R) at amino acid position 316 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