chr2-241852729-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005018.3(PDCD1):c.328G>A(p.Val110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005018.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDCD1 | NM_005018.3 | c.328G>A | p.Val110Met | missense_variant | Exon 2 of 5 | ENST00000334409.10 | NP_005009.2 | |
PDCD1 | XM_006712573.3 | c.328G>A | p.Val110Met | 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.328G>A | p.Val110Met | missense_variant | Exon 2 of 5 | 1 | NM_005018.3 | ENSP00000335062.5 | ||
PDCD1 | ENST00000343705.3 | c.157G>A | p.Val53Met | missense_variant | Exon 1 of 3 | 1 | ENSP00000340808.4 | |||
PDCD1 | ENST00000418831.1 | n.200+128G>A | intron_variant | Intron 2 of 4 | 1 | ENSP00000390296.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250566Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135676
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461626Hom.: 0 Cov.: 34 AF XY: 0.0000234 AC XY: 17AN XY: 727144
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.328G>A (p.V110M) alteration is located in exon 2 (coding exon 2) of the PDCD1 gene. This alteration results from a G to A substitution at nucleotide position 328, causing the valine (V) at amino acid position 110 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at