rs7910261
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012425.4(RSU1):c.282-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,169,496 control chromosomes in the GnomAD database, including 58,928 homozygotes. 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 0.42 ( 17639 hom., cov: 32)
Exomes 𝑓: 0.27 ( 41289 hom. )
Consequence
RSU1
NM_012425.4 intron
NM_012425.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.851
Genes affected
RSU1 (HGNC:10464): (Ras suppressor protein 1) This gene encodes a protein that is involved in the Ras signal transduction pathway, growth inhibition, and nerve-growth factor induced differentiation processes, as determined in mouse and human cell line studies. In mouse, the encoded protein was initially isolated based on its ability to inhibit v-Ras transformation. Multiple alternatively spliced transcript variants for this gene have been reported; one of these variants was found only in glioma tumors. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSU1 | NM_012425.4 | c.282-45T>C | intron_variant | ENST00000345264.10 | |||
RSU1 | NM_152724.3 | c.123-45T>C | intron_variant | ||||
RSU1 | XM_047425617.1 | c.282-45T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSU1 | ENST00000345264.10 | c.282-45T>C | intron_variant | 1 | NM_012425.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.417 AC: 63443AN: 152018Hom.: 17571 Cov.: 32
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GnomAD3 exomes AF: 0.298 AC: 69838AN: 234722Hom.: 12902 AF XY: 0.287 AC XY: 36459AN XY: 126898
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GnomAD4 exome AF: 0.267 AC: 271354AN: 1017360Hom.: 41289 Cov.: 13 AF XY: 0.264 AC XY: 138644AN XY: 524410
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GnomAD4 genome ? AF: 0.418 AC: 63579AN: 152136Hom.: 17639 Cov.: 32 AF XY: 0.412 AC XY: 30661AN XY: 74384
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at