rs10089937
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_024504.4(PRDM14):āc.1629T>Cā(p.Asp543=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 1,612,438 control chromosomes in the GnomAD database, including 317,336 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.62 ( 29629 hom., cov: 33)
Exomes š: 0.63 ( 287707 hom. )
Consequence
PRDM14
NM_024504.4 synonymous
NM_024504.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.519
Genes affected
PRDM14 (HGNC:14001): (PR/SET domain 14) This gene encodes a member of the PRDI-BF1 and RIZ homology domain containing (PRDM) family of transcriptional regulators. The encoded protein may possess histone methyltransferase activity and plays a critical role in cell pluripotency by suppressing the expression of differentiation marker genes. Expression of this gene may play a role in breast cancer. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
?
Synonymous conserved (PhyloP=-0.519 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM14 | NM_024504.4 | c.1629T>C | p.Asp543= | synonymous_variant | 8/8 | ENST00000276594.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM14 | ENST00000276594.3 | c.1629T>C | p.Asp543= | synonymous_variant | 8/8 | 1 | NM_024504.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.624 AC: 94830AN: 151976Hom.: 29590 Cov.: 33
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GnomAD3 exomes AF: 0.627 AC: 157495AN: 251086Hom.: 49983 AF XY: 0.628 AC XY: 85247AN XY: 135682
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GnomAD4 exome AF: 0.627 AC: 914929AN: 1460344Hom.: 287707 Cov.: 43 AF XY: 0.627 AC XY: 455750AN XY: 726444
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GnomAD4 genome ? AF: 0.624 AC: 94922AN: 152094Hom.: 29629 Cov.: 33 AF XY: 0.622 AC XY: 46231AN XY: 74352
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at