rs878854248

Variant summary

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

The NM_001134363.3(RBM20):​c.138_149delGCCGCCCCAGCC​(p.Pro47_Pro50del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000146 in 1,373,678 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P46P) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 1 hom. )

Consequence

RBM20
NM_001134363.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Publications

0 publications found
Variant links:
Genes affected
RBM20 (HGNC:27424): (RNA binding motif protein 20) This gene encodes a protein that binds RNA and regulates splicing. Mutations in this gene have been associated with familial dilated cardiomyopathy. [provided by RefSeq, Apr 2014]
RBM20 Gene-Disease associations (from GenCC):
  • dilated cardiomyopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • dilated cardiomyopathy 1DD
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
  • familial isolated dilated cardiomyopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • hypertrophic cardiomyopathy
    Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134363.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RBM20
NM_001134363.3
MANE Select
c.138_149delGCCGCCCCAGCCp.Pro47_Pro50del
disruptive_inframe_deletion
Exon 1 of 14NP_001127835.2

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RBM20
ENST00000369519.4
TSL:1 MANE Select
c.138_149delGCCGCCCCAGCCp.Pro47_Pro50del
disruptive_inframe_deletion
Exon 1 of 14ENSP00000358532.3
RBM20
ENST00000718239.1
c.138_149delGCCGCCCCAGCCp.Pro47_Pro50del
disruptive_inframe_deletion
Exon 1 of 14ENSP00000520684.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000146
AC:
2
AN:
1373678
Hom.:
1
AF XY:
0.00000295
AC XY:
2
AN XY:
677506
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
29332
American (AMR)
AF:
0.00
AC:
0
AN:
33976
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24436
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33984
South Asian (SAS)
AF:
0.0000258
AC:
2
AN:
77500
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40992
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4210
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1072264
Other (OTH)
AF:
0.00
AC:
0
AN:
56984
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs878854248; hg19: chr10-112404346; API