chr19-43578677-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001193621.3(PINLYP):c.158G>C(p.Cys53Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000217 in 1,383,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C53R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001193621.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PINLYP | NM_001193621.3 | c.158G>C | p.Cys53Ser | missense_variant | 3/6 | ENST00000599207.6 | |
PINLYP | XM_047438830.1 | c.230G>C | p.Cys77Ser | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PINLYP | ENST00000599207.6 | c.158G>C | p.Cys53Ser | missense_variant | 3/6 | 5 | NM_001193621.3 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000743 AC: 1AN: 134578Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 73296
GnomAD4 exome AF: 0.00000217 AC: 3AN: 1383688Hom.: 0 Cov.: 32 AF XY: 0.00000146 AC XY: 1AN XY: 682798
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.230G>C (p.C77S) alteration is located in exon 3 (coding exon 2) of the PINLYP gene. This alteration results from a G to C substitution at nucleotide position 230, causing the cysteine (C) at amino acid position 77 to be replaced by a serine (S). 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