X-15823079-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005089.4(ZRSR2):c.1286G>A(p.Arg429His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,208,232 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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 Uncertain significance (★).
Frequency
Consequence
NM_005089.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZRSR2 | NM_005089.4 | c.1286G>A | p.Arg429His | missense_variant | 11/11 | ENST00000307771.8 | |
ZRSR2 | XM_011545589.4 | c.1355G>A | p.Arg452His | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZRSR2 | ENST00000307771.8 | c.1286G>A | p.Arg429His | missense_variant | 11/11 | 1 | NM_005089.4 | P2 | |
ZRSR2 | ENST00000684799.1 | c.1208G>A | p.Arg403His | missense_variant | 10/11 | A2 | |||
ZRSR2 | ENST00000690252.1 | c.1286G>A | p.Arg429His | missense_variant, NMD_transcript_variant | 11/13 | ||||
ZRSR2 | ENST00000691502.1 | c.1172G>A | p.Arg391His | missense_variant, NMD_transcript_variant | 11/13 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112107Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1096125Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 361781
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112107Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1286G>A (p.R429H) alteration is located in exon 11 (coding exon 11) of the ZRSR2 gene. This alteration results from a G to A substitution at nucleotide position 1286, causing the arginine (R) at amino acid position 429 to be replaced by a histidine (H). 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