10-110667691-C-T

Variant names:

• chr10-110667691-C-T
• rs7082195
• NM_001134363.3:c.191+23046C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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 -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
RBM20	NM_001134363.3	c.191+23046C>T		intron_variant	Intron 1 of 13	ENST00000369519.4	NP_001127835.2
RBM20	XM_017016103.3	c.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
RBM20	ENST00000369519.4	c.191+23046C>T		intron_variant	Intron 1 of 13	1	NM_001134363.3	ENSP00000358532.3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22165 AN: 151988 Hom.: 1628 Cov.: 32

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

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

Other links and lift over

dbSNP: rs7082195; hg19: chr10-112427449;