chr5-123090181-C-CG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001136239.4(PRDM6):c.167_168insG(p.Pro58AlafsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,487,364 control chromosomes in the GnomAD database, including 53 homozygotes. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P56P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001136239.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM6 | NM_001136239.4 | c.167_168insG | p.Pro58AlafsTer6 | frameshift_variant | 2/8 | ENST00000407847.5 | |
PRDM6-AS1 | NR_146771.1 | n.135_136insC | non_coding_transcript_exon_variant | 1/2 | |||
PRDM6 | XM_047417878.1 | c.167_168insG | p.Pro58AlafsTer6 | frameshift_variant | 2/4 | ||
PRDM6 | XR_001742346.2 | n.461_462insG | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM6 | ENST00000407847.5 | c.167_168insG | p.Pro58AlafsTer6 | frameshift_variant | 2/8 | 5 | NM_001136239.4 | P1 | |
PRDM6-AS1 | ENST00000458103.2 | n.118_119insC | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1693AN: 151828Hom.: 31 Cov.: 33
GnomAD3 exomes AF: 0.000119 AC: 10AN: 84056Hom.: 0 AF XY: 0.000105 AC XY: 5AN XY: 47666
GnomAD4 exome AF: 0.000914 AC: 1220AN: 1335428Hom.: 21 Cov.: 42 AF XY: 0.000784 AC XY: 516AN XY: 658028
GnomAD4 genome ? AF: 0.0111 AC: 1692AN: 151936Hom.: 32 Cov.: 33 AF XY: 0.0103 AC XY: 768AN XY: 74296
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