rs3789604
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_018364.5(RSBN1):c.93A>T(p.Arg31=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,603,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
RSBN1
NM_018364.5 synonymous
NM_018364.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.00
Genes affected
RSBN1 (HGNC:25642): (round spermatid basic protein 1) Predicted to enable dioxygenase activity and metal ion binding activity. Predicted to be involved in chromatin organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP7
?
Synonymous conserved (PhyloP=-2 with no splicing effect.
BS2
?
High AC in GnomAdExome4 at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSBN1 | NM_018364.5 | c.93A>T | p.Arg31= | synonymous_variant | 1/7 | ENST00000261441.9 | |
RSBN1 | XM_017001518.3 | c.93A>T | p.Arg31= | synonymous_variant | 1/3 | ||
RSBN1 | NR_130896.2 | n.157A>T | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSBN1 | ENST00000261441.9 | c.93A>T | p.Arg31= | synonymous_variant | 1/7 | 2 | NM_018364.5 | P1 | |
RSBN1 | ENST00000612242.4 | c.93A>T | p.Arg31= | synonymous_variant | 1/7 | 2 | P1 | ||
RSBN1 | ENST00000615321.1 | upstream_gene_variant | 2 | ||||||
RSBN1 | ENST00000476412.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000853 AC: 2AN: 234336Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129046
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GnomAD4 exome AF: 0.0000296 AC: 43AN: 1451526Hom.: 0 Cov.: 33 AF XY: 0.0000332 AC XY: 24AN XY: 722582
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at