17-1830105-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002945.5(RPA1):c.12A>G(p.Gln4Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 1,249,336 control chromosomes in the GnomAD database, including 354,203 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002945.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPA1 | NM_002945.5 | c.12A>G | p.Gln4Gln | synonymous_variant | Exon 1 of 17 | ENST00000254719.10 | NP_002936.1 | |
RPA1 | NM_001355121.2 | c.12A>G | p.Gln4Gln | synonymous_variant | Exon 1 of 16 | NP_001342050.1 | ||
RPA1 | NM_001355120.2 | c.-36A>G | 5_prime_UTR_variant | Exon 1 of 17 | NP_001342049.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPA1 | ENST00000254719.10 | c.12A>G | p.Gln4Gln | synonymous_variant | Exon 1 of 17 | 1 | NM_002945.5 | ENSP00000254719.4 | ||
RPA1 | ENST00000570451 | c.-36A>G | 5_prime_UTR_variant | Exon 1 of 7 | 3 | ENSP00000459788.1 | ||||
SMYD4 | ENST00000571854.5 | c.-13+488T>C | intron_variant | Intron 1 of 4 | 4 | ENSP00000461089.1 | ||||
RPA1 | ENST00000571058.5 | c.-7+205A>G | intron_variant | Intron 1 of 5 | 4 | ENSP00000461733.1 |
Frequencies
GnomAD3 genomes AF: 0.681 AC: 103513AN: 151928Hom.: 36340 Cov.: 31
GnomAD3 exomes AF: 0.662 AC: 14278AN: 21576Hom.: 4873 AF XY: 0.667 AC XY: 6386AN XY: 9570
GnomAD4 exome AF: 0.755 AC: 828869AN: 1097292Hom.: 317840 Cov.: 50 AF XY: 0.754 AC XY: 391088AN XY: 518374
GnomAD4 genome AF: 0.681 AC: 103584AN: 152044Hom.: 36363 Cov.: 31 AF XY: 0.671 AC XY: 49852AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 67% of patients studied by a panel of primary immunodeficiencies. Number of patients: 64. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at