Variant 13-98176922-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_178861.5(RNF113B):c.315A>G(p.Pro105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 1,604,042 control chromosomes in the GnomAD database, including 676,470 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 0.78 ( 50659 hom., cov: 29)

Exomes 𝑓: 0.92 ( 625811 hom. )

Consequence

RNF113B
NM_178861.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.06

Variant links:

Genes affected

RNF113B (HGNC:17267): (ring finger protein 113B) Predicted to enable metal ion binding activity. Predicted to be involved in snoRNA splicing. Predicted to be part of U2-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

RNF113B links:

FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

FARP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-3.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RNF113B	NM_178861.5 linkuse as main transcript	c.315A>G	p.Pro105=	synonymous_variant	1/2	ENST00000267291.7	NP_849192.1
FARP1	NM_005766.4 linkuse as main transcript	c.-24+33430T>C		intron_variant		ENST00000319562.11	NP_005757.1
FARP1	NM_001001715.4 linkuse as main transcript	c.-24+33430T>C		intron_variant			NP_001001715.2
FARP1	NM_001286839.2 linkuse as main transcript	c.-24+34145T>C		intron_variant			NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF113B	ENST00000267291.7 linkuse as main transcript	c.315A>G	p.Pro105=	synonymous_variant	1/2	1	NM_178861.5	ENSP00000267291	P1
FARP1	ENST00000319562.11 linkuse as main transcript	c.-24+33430T>C		intron_variant		1	NM_005766.4	ENSP00000322926	P1	Q9Y4F1-1

Frequencies

GnomAD3 genomes

AF:

0.783

AC:

118826

AN:

151690

Hom.:

50659

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.950

Gnomad AMR

AF:

0.813

Gnomad ASJ

AF:

0.950

Gnomad EAS

AF:

0.934

Gnomad SAS

AF:

0.919

Gnomad FIN

AF:

0.962

Gnomad MID

AF:

0.873

Gnomad NFE

AF:

0.941

Gnomad OTH

AF:

0.817

GnomAD3 exomes

AF:

0.890

AC:

217872

AN:

244700

Hom.:

99290

AF XY:

0.903

AC XY:

120003

AN XY:

132862

show subpopulations

Gnomad AFR exome

AF:

0.399

Gnomad AMR exome

AF:

0.850

Gnomad ASJ exome

AF:

0.941

Gnomad EAS exome

AF:

0.945

Gnomad SAS exome

AF:

0.925

Gnomad FIN exome

AF:

0.958

Gnomad NFE exome

AF:

0.940

Gnomad OTH exome

AF:

0.913

GnomAD4 exome

AF:

0.924

AC:

1342277

AN:

1452234

Hom.:

625811

Cov.:

AF XY:

0.926

AC XY:

669502

AN XY:

722862

show subpopulations

Gnomad4 AFR exome

AF:

0.396

Gnomad4 AMR exome

AF:

0.849

Gnomad4 ASJ exome

AF:

0.944

Gnomad4 EAS exome

AF:

0.911

Gnomad4 SAS exome

AF:

0.929

Gnomad4 FIN exome

AF:

0.959

Gnomad4 NFE exome

AF:

0.943

Gnomad4 OTH exome

AF:

0.905

GnomAD4 genome

AF:

0.783

AC:

118860

AN:

151808

Hom.:

50659

Cov.:

AF XY:

0.786

AC XY:

58329

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.412

Gnomad4 AMR

AF:

0.813

Gnomad4 ASJ

AF:

0.950

Gnomad4 EAS

AF:

0.934

Gnomad4 SAS

AF:

0.919

Gnomad4 FIN

AF:

0.962

Gnomad4 NFE

AF:

0.941

Gnomad4 OTH

AF:

0.817

Alfa

AF:

0.922

Hom.:

89105

Bravo

AF:

0.757

Asia WGS

AF:

0.884

AC:

3075

AN:

3478

EpiCase

AF:

0.939

EpiControl

AF:

0.934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.85

DANN

Benign

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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