chr5-150125491-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2
The NM_002609.4(PDGFRB):c.1761G>T(p.Leu587=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L587L) has been classified as Likely benign.
Frequency
Consequence
NM_002609.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRB | NM_002609.4 | c.1761G>T | p.Leu587= | synonymous_variant | 12/23 | ENST00000261799.9 | |
PDGFRB | NM_001355016.2 | c.1569G>T | p.Leu523= | synonymous_variant | 11/22 | ||
PDGFRB | NM_001355017.2 | c.1278G>T | p.Leu426= | synonymous_variant | 12/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRB | ENST00000261799.9 | c.1761G>T | p.Leu587= | synonymous_variant | 12/23 | 1 | NM_002609.4 | P1 | |
PDGFRB | ENST00000520579.5 | c.*1075G>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/23 | 1 | ||||
PDGFRB | ENST00000520229.1 | n.30G>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251294Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135810
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461164Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726932
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at