rs1832745

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_001134363.3(RBM20):​c.2550+168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,116 control chromosomes in the GnomAD database, including 16,526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.45 ( 16526 hom., cov: 32)

Consequence

RBM20
NM_001134363.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.03
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 10-110813115-T-C is Benign according to our data. Variant chr10-110813115-T-C is described in ClinVar as [Benign]. Clinvar id is 671184.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RBM20NM_001134363.3 linkuse as main transcriptc.2550+168T>C intron_variant ENST00000369519.4 NP_001127835.2 Q5T481
RBM20XM_017016103.3 linkuse as main transcriptc.2385+168T>C intron_variant XP_016871592.1
RBM20XM_017016104.3 linkuse as main transcriptc.2166+168T>C intron_variant XP_016871593.1
RBM20XM_047425116.1 linkuse as main transcriptc.2166+168T>C intron_variant XP_047281072.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RBM20ENST00000369519.4 linkuse as main transcriptc.2550+168T>C intron_variant 1 NM_001134363.3 ENSP00000358532.3 Q5T481

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68797
AN:
151998
Hom.:
16522
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.272
Gnomad AMI
AF:
0.579
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.491
Gnomad EAS
AF:
0.535
Gnomad SAS
AF:
0.496
Gnomad FIN
AF:
0.544
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.518
Gnomad OTH
AF:
0.456
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.452
AC:
68832
AN:
152116
Hom.:
16526
Cov.:
32
AF XY:
0.458
AC XY:
34063
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.272
Gnomad4 AMR
AF:
0.531
Gnomad4 ASJ
AF:
0.491
Gnomad4 EAS
AF:
0.535
Gnomad4 SAS
AF:
0.495
Gnomad4 FIN
AF:
0.544
Gnomad4 NFE
AF:
0.518
Gnomad4 OTH
AF:
0.457
Alfa
AF:
0.509
Hom.:
19290
Bravo
AF:
0.443
Asia WGS
AF:
0.498
AC:
1731
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 15, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
CADD
Benign
9.4
DANN
Benign
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1832745; hg19: chr10-112572873; API