21-46402442-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006031.6(PCNT):āc.5074G>Cā(p.Val1692Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,614,114 control chromosomes in the GnomAD database, including 1 homozygotes. 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 ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1692I) has been classified as Likely benign.
Frequency
Consequence
NM_006031.6 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 | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.5074G>C | p.Val1692Leu | missense_variant | 27/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.4720G>C | p.Val1574Leu | missense_variant | 27/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.5074G>C | p.Val1692Leu | missense_variant | 27/47 | 1 | NM_006031.6 | P2 | |
PCNT | ENST00000480896.5 | c.4720G>C | p.Val1574Leu | missense_variant | 27/47 | 1 | A2 | ||
PCNT | ENST00000695558.1 | c.5107G>C | p.Val1703Leu | missense_variant | 28/48 | A2 | |||
PCNT | ENST00000703224.1 | c.*4317G>C | 3_prime_UTR_variant, NMD_transcript_variant | 29/49 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251478Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135920
GnomAD4 exome AF: 0.000103 AC: 151AN: 1461806Hom.: 1 Cov.: 31 AF XY: 0.0000908 AC XY: 66AN XY: 727200
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74468
ClinVar
Submissions by phenotype
PCNT-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 01, 2023 | The PCNT c.5074G>C variant is predicted to result in the amino acid substitution p.Val1692Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.011% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at