18-62113191-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_176787.5(PIGN):c.1377T>C(p.Ser459Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,610,870 control chromosomes in the GnomAD database, including 43,064 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_176787.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGN | NM_176787.5 | c.1377T>C | p.Ser459Ser | synonymous_variant | Exon 16 of 31 | ENST00000640252.2 | NP_789744.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGN | ENST00000640252.2 | c.1377T>C | p.Ser459Ser | synonymous_variant | Exon 16 of 31 | 1 | NM_176787.5 | ENSP00000492233.1 | ||
PIGN | ENST00000400334.7 | c.1377T>C | p.Ser459Ser | synonymous_variant | Exon 15 of 30 | 1 | ENSP00000383188.2 | |||
PIGN | ENST00000638424.1 | n.1377T>C | non_coding_transcript_exon_variant | Exon 14 of 29 | 5 | ENSP00000491963.1 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25712AN: 152060Hom.: 2929 Cov.: 32
GnomAD3 exomes AF: 0.177 AC: 43791AN: 246832Hom.: 4798 AF XY: 0.181 AC XY: 24222AN XY: 133870
GnomAD4 exome AF: 0.225 AC: 328421AN: 1458692Hom.: 40134 Cov.: 32 AF XY: 0.223 AC XY: 161916AN XY: 725620
GnomAD4 genome AF: 0.169 AC: 25717AN: 152178Hom.: 2930 Cov.: 32 AF XY: 0.166 AC XY: 12381AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Multiple congenital anomalies-hypotonia-seizures syndrome 1 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at