chr2-241851121-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005018.3(PDCD1):c.804T>C(p.Ala268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,612,824 control chromosomes in the GnomAD database, including 293,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A268A) has been classified as Likely benign.
Frequency
Consequence
NM_005018.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDCD1 | NM_005018.3 | c.804T>C | 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>C | p.Ala268= | synonymous_variant | 5/5 | 1 | NM_005018.3 | P1 | |
PDCD1 | ENST00000418831.1 | c.*367T>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.608 AC: 92431AN: 152000Hom.: 28361 Cov.: 33
GnomAD3 exomes AF: 0.632 AC: 157353AN: 249102Hom.: 50287 AF XY: 0.636 AC XY: 85918AN XY: 135056
GnomAD4 exome AF: 0.600 AC: 875807AN: 1460706Hom.: 264751 Cov.: 51 AF XY: 0.604 AC XY: 438894AN XY: 726674
GnomAD4 genome AF: 0.608 AC: 92526AN: 152118Hom.: 28401 Cov.: 33 AF XY: 0.620 AC XY: 46094AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 87% of patients studied by a panel of primary immunodeficiencies. Number of patients: 83. Only high quality variants are reported. - |
PDCD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at