5-123090090-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001136239.4(PRDM6):c.76C>T(p.Leu26Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000194 in 1,547,072 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001136239.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDM6 | NM_001136239.4 | c.76C>T | p.Leu26Phe | missense_variant | Exon 2 of 8 | ENST00000407847.5 | NP_001129711.1 | |
PRDM6 | XM_047417878.1 | c.76C>T | p.Leu26Phe | missense_variant | Exon 2 of 4 | XP_047273834.1 | ||
PRDM6-AS1 | NR_146771.1 | n.227G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||
PRDM6 | XR_001742346.2 | n.370C>T | non_coding_transcript_exon_variant | Exon 2 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 1 Cov.: 32
GnomAD4 exome AF: 7.17e-7 AC: 1AN: 1394918Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 688150
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152154Hom.: 1 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
PRDM6-related disorder Uncertain:1
The PRDM6 c.76C>T variant is predicted to result in the amino acid substitution p.Leu26Phe. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at