17-1872485-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002945.5(RPA1):c.413C>T(p.Ala138Val) 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 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002945.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPA1 | NM_002945.5 | c.413C>T | p.Ala138Val | missense_variant | Exon 6 of 17 | ENST00000254719.10 | NP_002936.1 | |
RPA1 | NM_001355120.2 | c.374C>T | p.Ala125Val | missense_variant | Exon 6 of 17 | NP_001342049.1 | ||
RPA1 | NM_001355121.2 | c.413C>T | p.Ala138Val | missense_variant | Exon 6 of 16 | NP_001342050.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPA1 | ENST00000254719.10 | c.413C>T | p.Ala138Val | missense_variant | Exon 6 of 17 | 1 | NM_002945.5 | ENSP00000254719.4 | ||
RPA1 | ENST00000570451.5 | c.374C>T | p.Ala125Val | missense_variant | Exon 6 of 7 | 3 | ENSP00000459788.1 | |||
RPA1 | ENST00000573924.1 | n.137C>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 4 | |||||
RPA1 | ENST00000571058.5 | c.*2C>T | downstream_gene_variant | 4 | ENSP00000461733.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727186
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.413C>T (p.A138V) alteration is located in exon 6 (coding exon 6) of the RPA1 gene. This alteration results from a C to T substitution at nucleotide position 413, causing the alanine (A) at amino acid position 138 to be replaced by a valine (V). 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