rs760605118

chr10-110644607-G-Cchr10-110644607-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6 BP7

The NM_001134363.3(RBM20):c.153G>C(p.Pro51=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P51P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000048 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RBM20 NM_001134363.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP6: Variant 10-110644607-G-C is Benign according to our data. Variant chr10-110644607-G-C is described in Lovd as [Likely_benign].
• BP7: Synonymous conserved (PhyloP=1.57 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM20	NM_001134363.3	c.153G>C	p.Pro51=	synonymous_variant	1/14	ENST00000369519.4
RBM20	XM_017016103.3	c.26+1167G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM20	ENST00000369519.4	c.153G>C	p.Pro51=	synonymous_variant	1/14	1	NM_001134363.3	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 7 AN: 145508 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.0000497

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000450

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000216

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000151

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00150 AC: 1411 AN: 939818 Hom.: 0 Cov.: 33 AF XY: 0.00140 AC XY: 660 AN XY: 472454

Gnomad4 AFR exome AF: 0.00214

Gnomad4 AMR exome AF: 0.000141

Gnomad4 ASJ exome AF: 0.000916

Gnomad4 EAS exome AF: 0.000491

Gnomad4 SAS exome AF: 0.000391

Gnomad4 FIN exome AF: 0.0000737

Gnomad4 NFE exome AF: 0.00175

Gnomad4 OTH exome AF: 0.00136

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000481 AC: 7 AN: 145652 Hom.: 0 Cov.: 32 AF XY: 0.0000282 AC XY: 2 AN XY: 71046

Gnomad4 AFR AF: 0.0000496

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000451

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000216

Gnomad4 NFE AF: 0.0000151

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	6.7
Dann	Benign	0.87

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: rs760605118; hg19: chr10-112404365;