rs375798246

chr10-110812544-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Moderate BS1_Supporting BS2

The NM_001134363.3(RBM20):c.2147G>A(p.Arg716Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 1,551,720 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R716W) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00025 (1 hom.)
• Consequence: RBM20 NM_001134363.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:10 B:1
• Conservation: PhyloP100: 7.25

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]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10744703).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000253 (354/1399412) while in subpopulation NFE AF= 0.00031 (335/1078976). AF 95% confidence interval is 0.000283. There are 1 homozygotes in gnomad4_exome. There are 175 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High AC in GnomAd at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM20	NM_001134363.3	c.2147G>A	p.Arg716Gln	missense_variant	9/14	ENST00000369519.4
RBM20	XM_017016103.3	c.1982G>A	p.Arg661Gln	missense_variant	9/14
RBM20	XM_017016104.3	c.1763G>A	p.Arg588Gln	missense_variant	9/14
RBM20	XM_047425116.1	c.1763G>A	p.Arg588Gln	missense_variant	9/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM20	ENST00000369519.4	c.2147G>A	p.Arg716Gln	missense_variant	9/14	1	NM_001134363.3	P1

Frequencies

GnomAD3 genomes AF: 0.0000723 AC: 11 AN: 152190 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000135 AC: 21 AN: 155108 Hom.: 0 AF XY: 0.000146 AC XY: 12 AN XY: 82272

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000351

Gnomad FIN exome AF: 0.0000630

Gnomad NFE exome AF: 0.000200

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000253 AC: 354 AN: 1399412 Hom.: 1 Cov.: 32 AF XY: 0.000254 AC XY: 175 AN XY: 690216

Gnomad4 AFR exome AF: 0.0000949

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000126

Gnomad4 FIN exome AF: 0.0000406

Gnomad4 NFE exome AF: 0.000310

Gnomad4 OTH exome AF: 0.0000690

GnomAD4 genome AF: 0.0000722 AC: 11 AN: 152308 Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5 AN XY: 74478

Gnomad4 AFR AF: 0.0000962

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000209 Hom.: 0

Bravo AF: 0.0000793

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000314 AC: 1

ExAC AF: 0.000235 AC: 6

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:10 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4

Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 24, 2016	The R716Q variant has been reported previously in an individual with DCM and was not present in 450 Caucasian control individuals (Li et al., 2010). Li et al., (2010) reports R716Q was subsequently identified in 17 of the individual's family members; however, only 8 individuals harboring R716Q were found to be affected and one individual with borderline DCM did not harbor the R716Q variant. The proband and many family members were also found to harbor an LMNA missense substitution. The R716Q variant was not observed with any significant frequency in approximately 2,300 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The R716Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is not conserved across species. In silico analysis predicts this variant likely does not alter the protein structure/function. Nevertheless, Guo et al., (2012) demonstrated that R716Q inactivates RBM20 activity in splice reporter assays. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 19, 2015	The p.Arg716Gln variant in RBM20 has been reported in 1 individual with DCM (Li 2010), which segregated with disease in 8 affected relatives and was identified in 2 relatives that verbally reported they had some cardiovascular abnormalities . However, 3 of the affected relatives also carried a second variant of unclear clinical significance in LMNA (p.Arg388His)(Parks 2008, Li 2010). Importantly, 1 affected relative and 2 relatives that verbally reported they had some cardiova scular abnormalities did not carry either variant. Our laboratory has detected t his variant in a 3 individuals (two adults who also carried an additional diseas e-causing variant and one child) with DCM, but did not segregate with disease in 2 affected relatives from one family (LMM unpublished data). These nonsegregati ons raise concern as to whether the RBM20 variant is disease-causing. This varia nt has also been identified in 2/8492 European chromosomes and 4/7910 South Asia n chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstit ute.org/; dbSNP rs375798246). The p.Arg716Gln variant lies within exon 9, which encodes a conserved protein domain where other pathogenic variants have been rep orted (Brauch 2009, Li 2010). However, the affected amino acid is poorly conserv ed in evolution, suggesting that a change at his position may be tolerated. Conv ersely, an in vitro splice reporter assay provided some evidence that the p.Arg7 16Gln variant may impact protein function (Guo 2012). However, these types of as says may not accurately represent biological function or disease mechanism. In s ummary, the clinical significance of the p.Arg716Gln variant is uncertain due to the conflicting data. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 21, 2021	Variant summary: RBM20 c.2147G>A (p.Arg716Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 155108 control chromosomes. The observed variant frequency is approximately 2.89 fold of the estimated maximal expected allele frequency for a pathogenic variant in RBM20 causing Dilated Cardiomyopathy phenotype (4.7e-05), suggesting that the variant is benign. c.2147G>A has been reported in the literature in individuals affected with Dilated Cardiomyopathy. In one large, well-phenotyped family, the variant was shown to segregate with disease in nine additional family members, however the variant was also present in three members who were clinically unaffected, and the variant was absent in three members who had clinical signs of DCM (Li_2010, Cowan_2018). In this family, several members also carried a second variant in the LMNA gene which may impact phenotype. Additionally, the LMM laboratory reports the variant to not segregate with disease in 2 affected relatives from one family (LMM unpublished data). The variant has also been reported in individual affected patients in the literature, without strong evidence for causality (Pugh_2014, Verdonschot_2020). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS. -

Dilated cardiomyopathy 1DD Uncertain:1 Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 20, 2024	- -

Cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Mar 02, 2017

- -

Primary dilated cardiomyopathy Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 12, 2022

The c.2147G>A (p.R716Q) alteration is located in exon 9 (coding exon 9) of the RBM20 gene. This alteration results from a G to A substitution at nucleotide position 2147, causing the arginine (R) at amino acid position 716 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.069	T
BayesDel_noAF	Uncertain	-0.030
Cadd	Pathogenic	28
Dann	Pathogenic	1.0
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.93	D
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-0.38	T
MutationTaster	Benign	0.91	D
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-1.5	N
REVEL	Uncertain	0.36
Sift	Uncertain	0.017	D
Sift4G	Benign	0.14	T
Vest4		0.29
MVP		0.40
ClinPred		0.22	T
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
gMVP		0.38

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

Other links and lift over

dbSNP: rs375798246; hg19: chr10-112572302;