9-5534858-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025239.4(PDCD1LG2):āc.169G>Cā(p.Ala57Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_025239.4 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 |
---|---|---|---|---|---|---|---|---|
PDCD1LG2 | NM_025239.4 | c.169G>C | p.Ala57Pro | missense_variant | Exon 3 of 7 | ENST00000397747.5 | NP_079515.2 | |
PDCD1LG2 | XM_005251600.4 | c.169G>C | p.Ala57Pro | missense_variant | Exon 3 of 7 | XP_005251657.1 | ||
LOC124902114 | XR_007061406.1 | n.162-10229C>G | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135866
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.169G>C (p.A57P) alteration is located in exon 3 (coding exon 2) of the PDCD1LG2 gene. This alteration results from a G to C substitution at nucleotide position 169, causing the alanine (A) at amino acid position 57 to be replaced by a proline (P). 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