chr4-54280489-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006206.6(PDGFRA):c.2323+7G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,455,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006206.6 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.2323+7G>C | splice_region_variant, intron_variant | ENST00000257290.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.2323+7G>C | splice_region_variant, intron_variant | 1 | NM_006206.6 | P1 | |||
PDGFRA | ENST00000509092.5 | n.2148G>C | non_coding_transcript_exon_variant | 15/15 | 1 | ||||
PDGFRA | ENST00000509490.5 | c.*244+7G>C | splice_region_variant, intron_variant, NMD_transcript_variant | 1 | |||||
PDGFRA | ENST00000507536.1 | n.749+7G>C | splice_region_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250396Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135420
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455082Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 724386
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at