chr11-117218490-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004716.4(PCSK7):c.1510C>T(p.Arg504Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,602,478 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_004716.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCSK7 | NM_004716.4 | c.1510C>T | p.Arg504Cys | missense_variant | 12/17 | ENST00000320934.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCSK7 | ENST00000320934.8 | c.1510C>T | p.Arg504Cys | missense_variant | 12/17 | 1 | NM_004716.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000285 AC: 7AN: 245220Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132684
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1450382Hom.: 0 Cov.: 28 AF XY: 0.0000139 AC XY: 10AN XY: 721754
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.1510C>T (p.R504C) alteration is located in exon 12 (coding exon 10) of the PCSK7 gene. This alteration results from a C to T substitution at nucleotide position 1510, causing the arginine (R) at amino acid position 504 to be replaced by a cysteine (C). 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