13-113196209-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001127202.4(PCID2):c.280G>A(p.Ala94Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,602,736 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001127202.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.280G>A | p.Ala94Thr | missense_variant | Exon 5 of 14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.280G>A | p.Ala94Thr | missense_variant | Exon 5 of 15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.280G>A | p.Ala94Thr | missense_variant | Exon 5 of 15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.274G>A | p.Ala92Thr | missense_variant | Exon 5 of 14 | 1 | ENSP00000364606.2 | |||
PCID2 | ENST00000375459.5 | c.274G>A | p.Ala92Thr | missense_variant | Exon 5 of 15 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251280Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135816
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1450572Hom.: 0 Cov.: 28 AF XY: 0.00000554 AC XY: 4AN XY: 721598
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.280G>A (p.A94T) alteration is located in exon 5 (coding exon 5) of the PCID2 gene. This alteration results from a G to A substitution at nucleotide position 280, causing the alanine (A) at amino acid position 94 to be replaced by a threonine (T). 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