Variant 22-45426007-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015653.5(RIBC2):c.735G>A(p.Leu245=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 1,612,828 control chromosomes in the GnomAD database, including 226,601 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 0.62 ( 31191 hom., cov: 33)

Exomes 𝑓: 0.51 ( 195410 hom. )

Consequence

RIBC2
NM_015653.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.76

Variant links:

Genes affected

RIBC2 (HGNC:13241): (RIB43A domain with coiled-coils 2) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RIBC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=2.76 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RIBC2	NM_015653.5 linkuse as main transcript	c.735G>A	p.Leu245=	synonymous_variant	5/7	ENST00000614167.2
RIBC2	XM_005261524.5 linkuse as main transcript	c.516G>A	p.Leu172=	synonymous_variant	5/7
RIBC2	XM_011530126.3 linkuse as main transcript	c.246G>A	p.Leu82=	synonymous_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIBC2	ENST00000614167.2 linkuse as main transcript	c.735G>A	p.Leu245=	synonymous_variant	5/7	1	NM_015653.5	P1
RIBC2	ENST00000466226.1 linkuse as main transcript	n.417G>A		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93632

AN:

151970

Hom.:

31143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.562

Gnomad AMR

AF:

0.575

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.614

GnomAD3 exomes

AF:

0.563

AC:

140851

AN:

250128

Hom.:

41588

AF XY:

0.563

AC XY:

76197

AN XY:

135314

show subpopulations

Gnomad AFR exome

AF:

0.883

Gnomad AMR exome

AF:

0.526

Gnomad ASJ exome

AF:

0.558

Gnomad EAS exome

AF:

0.704

Gnomad SAS exome

AF:

0.677

Gnomad FIN exome

AF:

0.494

Gnomad NFE exome

AF:

0.489

Gnomad OTH exome

AF:

0.546

GnomAD4 exome

AF:

0.509

AC:

743789

AN:

1460740

Hom.:

195410

Cov.:

AF XY:

0.512

AC XY:

372235

AN XY:

726610

show subpopulations

Gnomad4 AFR exome

AF:

0.890

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.555

Gnomad4 EAS exome

AF:

0.631

Gnomad4 SAS exome

AF:

0.667

Gnomad4 FIN exome

AF:

0.492

Gnomad4 NFE exome

AF:

0.477

Gnomad4 OTH exome

AF:

0.552

GnomAD4 genome

AF:

0.616

AC:

93740

AN:

152088

Hom.:

31191

Cov.:

AF XY:

0.619

AC XY:

46047

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.574

Gnomad4 ASJ

AF:

0.556

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.685

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.479

Gnomad4 OTH

AF:

0.618

Alfa

AF:

0.520

Hom.:

35502

Bravo

AF:

0.631

Asia WGS

AF:

0.751

AC:

2613

AN:

3478

EpiCase

AF:

0.497

EpiControl

AF:

0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.6

DANN

Benign

0.62

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