13-113181222-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001127202.4(PCID2):āc.694T>Gā(p.Tyr232Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000732 in 1,611,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001127202.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.694T>G | p.Tyr232Asp | missense_variant | Exon 10 of 14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.694T>G | p.Tyr232Asp | missense_variant | Exon 10 of 15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.694T>G | p.Tyr232Asp | missense_variant | Exon 10 of 15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.688T>G | p.Tyr230Asp | missense_variant | Exon 10 of 14 | 1 | ENSP00000364606.2 | |||
PCID2 | ENST00000375459.5 | c.688T>G | p.Tyr230Asp | missense_variant | Exon 10 of 15 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251220Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135804
GnomAD4 exome AF: 0.0000727 AC: 106AN: 1458812Hom.: 0 Cov.: 28 AF XY: 0.0000675 AC XY: 49AN XY: 726010
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.694T>G (p.Y232D) alteration is located in exon 10 (coding exon 10) of the PCID2 gene. This alteration results from a T to G substitution at nucleotide position 694, causing the tyrosine (Y) at amino acid position 232 to be replaced by an aspartic acid (D). 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