chrX-96884635-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013347.4(RPA4):c.325G>C(p.Gly109Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,097,549 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013347.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPA4 | NM_013347.4 | c.325G>C | p.Gly109Arg | missense_variant | 1/1 | ENST00000373040.4 | |
DIAPH2 | NM_006729.5 | c.587+2917G>C | intron_variant | ENST00000324765.13 | |||
DIAPH2 | NM_007309.4 | c.587+2917G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPA4 | ENST00000373040.4 | c.325G>C | p.Gly109Arg | missense_variant | 1/1 | NM_013347.4 | P1 | ||
DIAPH2 | ENST00000324765.13 | c.587+2917G>C | intron_variant | 1 | NM_006729.5 | A2 | |||
DIAPH2 | ENST00000373049.8 | c.587+2917G>C | intron_variant | 1 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD3 exomes AF: 0.000148 AC: 27AN: 182819Hom.: 0 AF XY: 0.0000890 AC XY: 6AN XY: 67441
GnomAD4 exome AF: 0.0000282 AC: 31AN: 1097549Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 6AN XY: 362915
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.325G>C (p.G109R) alteration is located in exon 1 (coding exon 1) of the RPA4 gene. This alteration results from a G to C substitution at nucleotide position 325, causing the glycine (G) at amino acid position 109 to be replaced by an arginine (R). 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