Variant rs11256802 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032905.5(RBM17):c.506-148A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 555,128 control chromosomes in the GnomAD database, including 2,674 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 0.094 ( 745 hom., cov: 31)

Exomes 𝑓: 0.090 ( 1929 hom. )

Consequence

RBM17
NM_032905.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.629

Variant links:

Genes affected

RBM17 (HGNC:16944): (RNA binding motif protein 17) This gene encodes an RNA binding protein. The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 9 and 15. [provided by RefSeq, Mar 2009]

RBM17 links:

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM17	NM_032905.5 linkuse as main transcript	c.506-148A>C		intron_variant		ENST00000379888.9	NP_116294.1
RBM17	NM_001145547.2 linkuse as main transcript	c.506-148A>C		intron_variant			NP_001139019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM17	ENST00000379888.9 linkuse as main transcript	c.506-148A>C		intron_variant		1	NM_032905.5	ENSP00000369218	P1

Frequencies

GnomAD3 genomes

AF:

0.0944

AC:

14336

AN:

151924

Hom.:

744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0828

Gnomad ASJ

AF:

0.0666

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0910

Gnomad FIN

AF:

0.0824

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0796

Gnomad OTH

AF:

0.0953

GnomAD4 exome

AF:

0.0900

AC:

36278

AN:

403086

Hom.:

1929

Cov.:

AF XY:

0.0895

AC XY:

19031

AN XY:

212592

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0588

Gnomad4 ASJ exome

AF:

0.0690

Gnomad4 EAS exome

AF:

0.190

Gnomad4 SAS exome

AF:

0.0871

Gnomad4 FIN exome

AF:

0.0848

Gnomad4 NFE exome

AF:

0.0806

Gnomad4 OTH exome

AF:

0.0998

GnomAD4 genome

AF:

0.0944

AC:

14354

AN:

152042

Hom.:

745

Cov.:

AF XY:

0.0953

AC XY:

7085

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.119

Gnomad4 AMR

AF:

0.0827

Gnomad4 ASJ

AF:

0.0666

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.0915

Gnomad4 FIN

AF:

0.0824

Gnomad4 NFE

AF:

0.0796

Gnomad4 OTH

AF:

0.0972

Alfa

AF:

0.0765

Hom.:

491

Bravo

AF:

0.0948

Asia WGS

AF:

0.136

AC:

473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.5

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over