GeneBe

rs56715139

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_012425.4(RSU1):​c.599-8_599-3delCCCCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,076,450 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 17)
Exomes 𝑓: 0.0000019 ( 0 hom. )

Consequence

RSU1
NM_012425.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.45

Publications

0 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RSU1NM_012425.4 linkc.599-8_599-3delCCCCCC splice_region_variant, intron_variant Intron 7 of 8 ENST00000345264.10 NP_036557.1 Q15404-1
RSU1NM_152724.3 linkc.440-8_440-3delCCCCCC splice_region_variant, intron_variant Intron 6 of 7 NP_689937.2 Q15404-2
RSU1XM_047425617.1 linkc.598+57376_598+57381delCCCCCC intron_variant Intron 6 of 6 XP_047281573.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RSU1ENST00000345264.10 linkc.599-8_599-3delCCCCCC splice_region_variant, intron_variant Intron 7 of 8 1 NM_012425.4 ENSP00000339521.5 Q15404-1

Frequencies

GnomAD3 genomes
Cov.:
17
GnomAD4 exome
AF:
0.00000186
AC:
2
AN:
1076450
Hom.:
0
AF XY:
0.00000187
AC XY:
1
AN XY:
534766
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
25580
American (AMR)
AF:
0.0000722
AC:
2
AN:
27684
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17980
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28672
South Asian (SAS)
AF:
0.00
AC:
0
AN:
60918
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35862
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4334
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
831504
Other (OTH)
AF:
0.00
AC:
0
AN:
43916
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.250
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56715139; hg19: chr10-16737156; API