chr3-170270533-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002740.6(PRKCI):āc.563T>Cā(p.Ile188Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,028 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 (ā ).
Frequency
Consequence
NM_002740.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCI | NM_002740.6 | c.563T>C | p.Ile188Thr | missense_variant | 6/18 | ENST00000295797.5 | |
PRKCI | XM_047448575.1 | c.221T>C | p.Ile74Thr | missense_variant | 5/17 | ||
PRKCI | XM_047448574.1 | c.563T>C | p.Ile188Thr | missense_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCI | ENST00000295797.5 | c.563T>C | p.Ile188Thr | missense_variant | 6/18 | 1 | NM_002740.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 151776Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 250958Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135718
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461154Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 726906
GnomAD4 genome AF: 0.000316 AC: 48AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.000337 AC XY: 25AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.563T>C (p.I188T) alteration is located in exon 6 (coding exon 6) of the PRKCI gene. This alteration results from a T to C substitution at nucleotide position 563, causing the isoleucine (I) at amino acid position 188 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