2-241852361-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005018.3(PDCD1):c.437-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,553,738 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_005018.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDCD1 | NM_005018.3 | c.437-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000334409.10 | |||
PDCD1 | XM_006712573.3 | c.437-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDCD1 | ENST00000334409.10 | c.437-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005018.3 | P1 | |||
PDCD1 | ENST00000343705.3 | c.266+260C>T | intron_variant | 1 | |||||
PDCD1 | ENST00000418831.1 | c.*-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151884Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 228380Hom.: 0 AF XY: 0.00000796 AC XY: 1AN XY: 125674
GnomAD4 exome AF: 0.00000571 AC: 8AN: 1401854Hom.: 0 Cov.: 24 AF XY: 0.00000430 AC XY: 3AN XY: 697950
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151884Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5AN XY: 74188
ClinVar
Submissions by phenotype
PDCD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at