rs2270412
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002945.5(RPA1):c.1551+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,599,184 control chromosomes in the GnomAD database, including 35,215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002945.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPA1 | NM_002945.5 | c.1551+29G>A | intron_variant | Intron 14 of 16 | ENST00000254719.10 | NP_002936.1 | ||
RPA1 | NM_001355120.2 | c.1512+29G>A | intron_variant | Intron 14 of 16 | NP_001342049.1 | |||
RPA1 | NM_001355121.2 | c.1375-2953G>A | intron_variant | Intron 13 of 15 | NP_001342050.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25691AN: 152084Hom.: 2746 Cov.: 32
GnomAD3 exomes AF: 0.215 AC: 52365AN: 243968Hom.: 5927 AF XY: 0.216 AC XY: 28442AN XY: 131666
GnomAD4 exome AF: 0.208 AC: 300895AN: 1446982Hom.: 32474 Cov.: 31 AF XY: 0.209 AC XY: 149956AN XY: 717836
GnomAD4 genome AF: 0.169 AC: 25690AN: 152202Hom.: 2741 Cov.: 32 AF XY: 0.173 AC XY: 12845AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 43% of patients studied by a panel of primary immunodeficiencies. Number of patients: 41. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at