2-241852716-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005018.3(PDCD1):c.341G>A(p.Arg114Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005018.3 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDCD1 | NM_005018.3 | c.341G>A | p.Arg114Gln | missense_variant | Exon 2 of 5 | ENST00000334409.10 | NP_005009.2 | |
PDCD1 | XM_006712573.3 | c.341G>A | p.Arg114Gln | missense_variant | Exon 2 of 4 | XP_006712636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDCD1 | ENST00000334409.10 | c.341G>A | p.Arg114Gln | missense_variant | Exon 2 of 5 | 1 | NM_005018.3 | ENSP00000335062.5 | ||
PDCD1 | ENST00000343705.3 | c.170G>A | p.Arg57Gln | missense_variant | Exon 1 of 3 | 1 | ENSP00000340808.4 | |||
PDCD1 | ENST00000418831.1 | n.200+141G>A | intron_variant | Intron 2 of 4 | 1 | ENSP00000390296.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250432Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135608
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461506Hom.: 0 Cov.: 34 AF XY: 0.0000330 AC XY: 24AN XY: 727084
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at