chr12-55955822-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001384361.1(PMEL):c.1513G>A(p.Gly505Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00428 in 1,614,050 control chromosomes in the GnomAD database, including 269 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G505D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001384361.1 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 |
---|---|---|---|---|---|---|---|
PMEL | NM_001384361.1 | c.1513G>A | p.Gly505Ser | missense_variant | 8/11 | ENST00000548747.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMEL | ENST00000548747.6 | c.1513G>A | p.Gly505Ser | missense_variant | 8/11 | 1 | NM_001384361.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0234 AC: 3553AN: 152112Hom.: 143 Cov.: 32
GnomAD3 exomes AF: 0.00607 AC: 1526AN: 251438Hom.: 66 AF XY: 0.00425 AC XY: 578AN XY: 135902
GnomAD4 exome AF: 0.00229 AC: 3345AN: 1461820Hom.: 123 Cov.: 31 AF XY: 0.00189 AC XY: 1371AN XY: 727220
GnomAD4 genome ? AF: 0.0235 AC: 3570AN: 152230Hom.: 146 Cov.: 32 AF XY: 0.0232 AC XY: 1730AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at