6-28504476-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182701.1(GPX6):āc.482A>Gā(p.Asp161Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00646 in 1,613,984 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_182701.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPX6 | NM_182701.1 | c.482A>G | p.Asp161Gly | missense_variant | 5/5 | ENST00000361902.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPX6 | ENST00000361902.5 | c.482A>G | p.Asp161Gly | missense_variant | 5/5 | 1 | NM_182701.1 | P1 | |
GPX6 | ENST00000474923.1 | c.382A>G | p.Ile128Val | missense_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0122 AC: 1857AN: 152102Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00785 AC: 1960AN: 249544Hom.: 18 AF XY: 0.00739 AC XY: 1000AN XY: 135388
GnomAD4 exome AF: 0.00586 AC: 8569AN: 1461764Hom.: 79 Cov.: 31 AF XY: 0.00588 AC XY: 4278AN XY: 727174
GnomAD4 genome AF: 0.0122 AC: 1859AN: 152220Hom.: 18 Cov.: 32 AF XY: 0.0119 AC XY: 882AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at