Variant chr22-45426037-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_015653.5(RIBC2):c.765C>T(p.Asp255=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00512 in 1,614,012 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 3 hom., cov: 34)

Exomes 𝑓: 0.0052 ( 28 hom. )

Consequence

RIBC2
NM_015653.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.939

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 -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 22-45426037-C-T is Benign according to our data. Variant chr22-45426037-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653287.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.939 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RIBC2	NM_015653.5 linkuse as main transcript	c.765C>T	p.Asp255=	synonymous_variant	5/7	ENST00000614167.2
RIBC2	XM_005261524.5 linkuse as main transcript	c.546C>T	p.Asp182=	synonymous_variant	5/7
RIBC2	XM_011530126.3 linkuse as main transcript	c.276C>T	p.Asp92=	synonymous_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIBC2	ENST00000614167.2 linkuse as main transcript	c.765C>T	p.Asp255=	synonymous_variant	5/7	1	NM_015653.5	P1
RIBC2	ENST00000466226.1 linkuse as main transcript	n.447C>T		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes

AF:

0.00406

AC:

618

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00414

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00566

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00448

AC:

1124

AN:

250750

Hom.:

AF XY:

0.00434

AC XY:

589

AN XY:

135710

show subpopulations

Gnomad AFR exome

AF:

0.000864

Gnomad AMR exome

AF:

0.00330

Gnomad ASJ exome

AF:

0.00886

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00288

Gnomad FIN exome

AF:

0.00500

Gnomad NFE exome

AF:

0.00600

Gnomad OTH exome

AF:

0.00523

GnomAD4 exome

AF:

0.00523

AC:

7640

AN:

1461682

Hom.:

Cov.:

AF XY:

0.00511

AC XY:

3712

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.000836

Gnomad4 AMR exome

AF:

0.00304

Gnomad4 ASJ exome

AF:

0.00804

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00266

Gnomad4 FIN exome

AF:

0.00529

Gnomad4 NFE exome

AF:

0.00575

Gnomad4 OTH exome

AF:

0.00523

GnomAD4 genome

AF:

0.00405

AC:

617

AN:

152330

Hom.:

Cov.:

AF XY:

0.00395

AC XY:

294

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00414

Gnomad4 NFE

AF:

0.00566

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00498

Hom.:

Bravo

AF:

0.00383

EpiCase

AF:

0.00551

EpiControl

AF:

0.00611

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

RIBC2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

8.2

DANN

Benign

0.66

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over