13-113208624-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001127202.4(PCID2):āc.11T>Cā(p.Ile4Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000106 in 1,607,148 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.11T>C | p.Ile4Thr | missense_variant | Exon 1 of 14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.11T>C | p.Ile4Thr | missense_variant | Exon 1 of 15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.11T>C | p.Ile4Thr | missense_variant | Exon 1 of 15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.-571T>C | 5_prime_UTR_variant | Exon 1 of 14 | 1 | ENSP00000364606.2 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151362Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236490Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129390
GnomAD4 exome AF: 0.00000824 AC: 12AN: 1455666Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 2AN XY: 723942
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151482Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74046
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11T>C (p.I4T) alteration is located in exon 1 (coding exon 1) of the PCID2 gene. This alteration results from a T to C substitution at nucleotide position 11, causing the isoleucine (I) at amino acid position 4 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