4-151100479-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001006.5(RPS3A):c.63-6A>T 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 0.00587 in 1,507,156 control chromosomes in the GnomAD database, including 363 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_001006.5 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 |
---|---|---|---|---|---|---|---|
RPS3A | NM_001006.5 | c.63-6A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000274065.9 | |||
RPS3A | NM_001267699.2 | c.63-6A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS3A | ENST00000274065.9 | c.63-6A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001006.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0279 AC: 4242AN: 152220Hom.: 196 Cov.: 33
GnomAD3 exomes AF: 0.00782 AC: 1958AN: 250258Hom.: 81 AF XY: 0.00589 AC XY: 797AN XY: 135312
GnomAD4 exome AF: 0.00339 AC: 4588AN: 1354818Hom.: 167 Cov.: 20 AF XY: 0.00306 AC XY: 2083AN XY: 680562
GnomAD4 genome AF: 0.0280 AC: 4265AN: 152338Hom.: 196 Cov.: 33 AF XY: 0.0267 AC XY: 1986AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at