chr21-41815763-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001040424.3(PRDM15):c.2334G>C(p.Glu778Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040424.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM15 | NM_001040424.3 | c.2334G>C | p.Glu778Asp | missense_variant | 19/24 | ENST00000398548.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM15 | ENST00000398548.6 | c.2334G>C | p.Glu778Asp | missense_variant | 19/24 | 1 | NM_001040424.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000519 AC: 79AN: 152278Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251362Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135882
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 727188
GnomAD4 genome ? AF: 0.000519 AC: 79AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000484 AC XY: 36AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.3432G>C (p.E1144D) alteration is located in exon 26 (coding exon 26) of the PRDM15 gene. This alteration results from a G to C substitution at nucleotide position 3432, causing the glutamic acid (E) at amino acid position 1144 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at