rs2227981
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_005018.3(PDCD1):c.804T>G(p.Ala268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,612,964 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A268A) has been classified as Benign.
Frequency
Consequence
NM_005018.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDCD1 | NM_005018.3 | c.804T>G | p.Ala268= | synonymous_variant | 5/5 | ENST00000334409.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDCD1 | ENST00000334409.10 | c.804T>G | p.Ala268= | synonymous_variant | 5/5 | 1 | NM_005018.3 | P1 | |
PDCD1 | ENST00000418831.1 | c.*367T>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000697 AC: 106AN: 152030Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000157 AC: 39AN: 249102Hom.: 1 AF XY: 0.000141 AC XY: 19AN XY: 135056
GnomAD4 exome AF: 0.0000685 AC: 100AN: 1460816Hom.: 3 Cov.: 51 AF XY: 0.0000537 AC XY: 39AN XY: 726730
GnomAD4 genome ? AF: 0.000697 AC: 106AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.000672 AC XY: 50AN XY: 74378
ClinVar
Submissions by phenotype
PDCD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2020 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | PDCD1: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at