chr19-32991938-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033103.5(RHPN2):c.1529G>A(p.Arg510Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033103.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHPN2 | NM_033103.5 | c.1529G>A | p.Arg510Gln | missense_variant | 13/15 | ENST00000254260.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHPN2 | ENST00000254260.8 | c.1529G>A | p.Arg510Gln | missense_variant | 13/15 | 1 | NM_033103.5 | P1 | |
RHPN2 | ENST00000544458.6 | n.1858G>A | non_coding_transcript_exon_variant | 10/12 | 2 | ||||
RHPN2 | ENST00000591502.1 | n.208G>A | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
RHPN2 | ENST00000588388.5 | c.*1066G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250936Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135644
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461648Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727132
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 05, 2023 | The c.1529G>A (p.R510Q) alteration is located in exon 13 (coding exon 13) of the RHPN2 gene. This alteration results from a G to A substitution at nucleotide position 1529, causing the arginine (R) at amino acid position 510 to be replaced by a glutamine (Q). 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