rs77287813
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020227.4(PRDM9):c.2368A>C(p.Asn790His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 1,436,540 control chromosomes in the GnomAD database, including 454 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_020227.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRDM9 | ENST00000296682.4 | c.2368A>C | p.Asn790His | missense_variant | Exon 11 of 11 | 1 | NM_020227.4 | ENSP00000296682.4 | ||
PRDM9 | ENST00000502755.6 | c.2368A>C | p.Asn790His | missense_variant | Exon 11 of 11 | 4 | ENSP00000425471.2 |
Frequencies
GnomAD3 genomes AF: 0.0171 AC: 1713AN: 100376Hom.: 25 Cov.: 18
GnomAD3 exomes AF: 0.0232 AC: 4974AN: 213972Hom.: 56 AF XY: 0.0229 AC XY: 2681AN XY: 117326
GnomAD4 exome AF: 0.0221 AC: 29502AN: 1336156Hom.: 429 Cov.: 40 AF XY: 0.0220 AC XY: 14663AN XY: 665838
GnomAD4 genome AF: 0.0170 AC: 1711AN: 100384Hom.: 25 Cov.: 18 AF XY: 0.0179 AC XY: 845AN XY: 47242
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at