3-142818389-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013363.4(PCOLCE2):c.1194G>A(p.Met398Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013363.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCOLCE2 | NM_013363.4 | c.1194G>A | p.Met398Ile | missense_variant | 9/9 | ENST00000295992.8 | NP_037495.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCOLCE2 | ENST00000295992.8 | c.1194G>A | p.Met398Ile | missense_variant | 9/9 | 1 | NM_013363.4 | ENSP00000295992 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249404Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134976
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461210Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726958
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2022 | The c.1194G>A (p.M398I) alteration is located in exon 9 (coding exon 9) of the PCOLCE2 gene. This alteration results from a G to A substitution at nucleotide position 1194, causing the methionine (M) at amino acid position 398 to be replaced by an isoleucine (I). 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