chr15-75676580-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001897.5(CSPG4):c.5939G>A(p.Arg1980His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00396 in 1,613,092 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001897.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSPG4 | NM_001897.5 | c.5939G>A | p.Arg1980His | missense_variant | 10/10 | ENST00000308508.5 | |
CSPG4 | XM_047432196.1 | c.4877G>A | p.Arg1626His | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSPG4 | ENST00000308508.5 | c.5939G>A | p.Arg1980His | missense_variant | 10/10 | 1 | NM_001897.5 | P1 | |
ENST00000569467.1 | n.354C>T | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00288 AC: 438AN: 152204Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00296 AC: 737AN: 249124Hom.: 2 AF XY: 0.00308 AC XY: 416AN XY: 135062
GnomAD4 exome AF: 0.00407 AC: 5942AN: 1460770Hom.: 20 Cov.: 32 AF XY: 0.00398 AC XY: 2893AN XY: 726686
GnomAD4 genome ? AF: 0.00288 AC: 438AN: 152322Hom.: 2 Cov.: 33 AF XY: 0.00250 AC XY: 186AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | CSPG4: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at