10-110667691-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001134363.3(RBM20):​c.191+23046C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,106 control chromosomes in the GnomAD database, including 1,637 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 0.15 ( 1637 hom., cov: 32)

Consequence

RBM20
NM_001134363.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.289
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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RBM20NM_001134363.3 linkc.191+23046C>T intron_variant Intron 1 of 13 ENST00000369519.4 NP_001127835.2 Q5T481
RBM20XM_017016103.3 linkc.26+24251C>T intron_variant Intron 1 of 13 XP_016871592.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RBM20ENST00000369519.4 linkc.191+23046C>T intron_variant Intron 1 of 13 1 NM_001134363.3 ENSP00000358532.3 Q5T481

Frequencies

GnomAD3 genomes
AF:
0.146
AC:
22165
AN:
151988
Hom.:
1628
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.127
Gnomad AMI
AF:
0.171
Gnomad AMR
AF:
0.155
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.0969
Gnomad SAS
AF:
0.149
Gnomad FIN
AF:
0.111
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.165
Gnomad OTH
AF:
0.149
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22206
AN:
152106
Hom.:
1637
Cov.:
32
AF XY:
0.146
AC XY:
10820
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.0971
Gnomad4 SAS
AF:
0.149
Gnomad4 FIN
AF:
0.111
Gnomad4 NFE
AF:
0.165
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.150
Hom.:
1823
Bravo
AF:
0.146
Asia WGS
AF:
0.150
AC:
523
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.7
DANN
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs7082195; hg19: chr10-112427449; API