1-17381130-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207421.4(PADI6):āc.519G>Cā(p.Glu173Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000876 in 1,609,154 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207421.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI6 | NM_207421.4 | c.519G>C | p.Glu173Asp | missense_variant | 5/16 | ENST00000619609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI6 | ENST00000619609.1 | c.519G>C | p.Glu173Asp | missense_variant | 5/16 | 1 | NM_207421.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000623 AC: 15AN: 240878Hom.: 0 AF XY: 0.0000613 AC XY: 8AN XY: 130450
GnomAD4 exome AF: 0.0000885 AC: 129AN: 1456932Hom.: 1 Cov.: 31 AF XY: 0.0000884 AC XY: 64AN XY: 724168
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74422
ClinVar
Submissions by phenotype
Premature ovarian failure Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Apr 22, 2019 | This variant was identified as homozygous in a female individual with hypergonadotropic hypogonadism. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at