X-96884878-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_013347.4(RPA4):c.568G>T(p.Ala190Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000433 in 1,208,985 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 156 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013347.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPA4 | NM_013347.4 | c.568G>T | p.Ala190Ser | missense_variant | 1/1 | ENST00000373040.4 | |
DIAPH2 | NM_006729.5 | c.587+3160G>T | intron_variant | ENST00000324765.13 | |||
DIAPH2 | NM_007309.4 | c.587+3160G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPA4 | ENST00000373040.4 | c.568G>T | p.Ala190Ser | missense_variant | 1/1 | NM_013347.4 | P1 | ||
DIAPH2 | ENST00000324765.13 | c.587+3160G>T | intron_variant | 1 | NM_006729.5 | A2 | |||
DIAPH2 | ENST00000373049.8 | c.587+3160G>T | intron_variant | 1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 15AN: 111211Hom.: 0 Cov.: 21 AF XY: 0.000150 AC XY: 5AN XY: 33369
GnomAD3 exomes AF: 0.000126 AC: 23AN: 183206Hom.: 0 AF XY: 0.0000886 AC XY: 6AN XY: 67706
GnomAD4 exome AF: 0.000463 AC: 508AN: 1097774Hom.: 0 Cov.: 31 AF XY: 0.000416 AC XY: 151AN XY: 363136
GnomAD4 genome ? AF: 0.000135 AC: 15AN: 111211Hom.: 0 Cov.: 21 AF XY: 0.000150 AC XY: 5AN XY: 33369
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.568G>T (p.A190S) alteration is located in exon 1 (coding exon 1) of the RPA4 gene. This alteration results from a G to T substitution at nucleotide position 568, causing the alanine (A) at amino acid position 190 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | RPA4: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at