chr15-75676844-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001897.5(CSPG4):c.5675C>G(p.Thr1892Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000384 in 1,561,500 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 (★).
Frequency
Consequence
NM_001897.5 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 |
---|---|---|---|---|---|---|---|
CSPG4 | NM_001897.5 | c.5675C>G | p.Thr1892Ser | missense_variant | 10/10 | ENST00000308508.5 | |
CSPG4 | XM_047432196.1 | c.4613C>G | p.Thr1538Ser | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSPG4 | ENST00000308508.5 | c.5675C>G | p.Thr1892Ser | missense_variant | 10/10 | 1 | NM_001897.5 | P1 | |
ENST00000569467.1 | n.510+108G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000969 AC: 2AN: 206488Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 112990
GnomAD4 exome AF: 7.10e-7 AC: 1AN: 1409252Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1AN XY: 696288
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.5675C>G (p.T1892S) alteration is located in exon 10 (coding exon 10) of the CSPG4 gene. This alteration results from a C to G substitution at nucleotide position 5675, causing the threonine (T) at amino acid position 1892 to be replaced by a serine (S). 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