chr17-1842798-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002945.5(RPA1):c.34-5C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,613,908 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002945.5 splice_region, splice_polypyrimidine_tract, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPA1 | NM_002945.5 | c.34-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000254719.10 | |||
RPA1 | NM_001355120.2 | c.-6-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
RPA1 | NM_001355121.2 | c.34-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPA1 | ENST00000254719.10 | c.34-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002945.5 | P1 | |||
RPA1 | ENST00000570451.5 | c.-6-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
RPA1 | ENST00000571058.5 | c.-6-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0109 AC: 1665AN: 152116Hom.: 36 Cov.: 31
GnomAD3 exomes AF: 0.00290 AC: 730AN: 251428Hom.: 14 AF XY: 0.00213 AC XY: 290AN XY: 135898
GnomAD4 exome AF: 0.00112 AC: 1643AN: 1461674Hom.: 30 Cov.: 30 AF XY: 0.000993 AC XY: 722AN XY: 727140
GnomAD4 genome ? AF: 0.0110 AC: 1668AN: 152234Hom.: 36 Cov.: 31 AF XY: 0.0108 AC XY: 805AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at