Variant chr22-50769106-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001130919.3(RABL2B):c.526C>T(p.Arg176Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00030 ( 0 hom., cov: 17)

Exomes 𝑓: 0.00025 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

RABL2B
NM_001130919.3 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.10

Variant links:

Genes affected

RABL2B (HGNC:9800): (RAB, member of RAS oncogene family like 2B) The RABL2B protein is a member of the RAB gene family which belongs to the RAS GTPase superfamily. RABL2B is located within a subtelomeric region of 22q13.3. Multiple alternatively spliced transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

RABL2B links:

RPL23AP7 (HGNC:):

RPL23AP7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 22-50769106-G-A is Benign according to our data. Variant chr22-50769106-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 719849.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RABL2B	NM_001130919.3 linkuse as main transcript	c.526C>T	p.Arg176Ter	stop_gained	8/9	ENST00000691320.1
RPL23AP82	NR_026981.1 linkuse as main transcript	n.241+11780G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABL2B	ENST00000691320.1 linkuse as main transcript	c.526C>T	p.Arg176Ter	stop_gained	8/9		NM_001130919.3	A2	Q9UNT1-2
RPL23AP7	ENST00000496652.5 linkuse as main transcript	n.379+11780G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

131454

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000295

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000804

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000216

Gnomad SAS

AF:

0.000282

Gnomad FIN

AF:

0.00377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000639

Gnomad OTH

AF:

0.000607

GnomAD3 exomes

AF:

0.000493

AC:

AN:

89188

Hom.:

AF XY:

0.000312

AC XY:

AN XY:

44900

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000746

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000202

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00286

Gnomad NFE exome

AF:

0.0000323

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000250

AC:

173

AN:

691946

Hom.:

Cov.:

AF XY:

0.000199

AC XY:

AN XY:

356710

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000732

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000308

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00250

Gnomad4 NFE exome

AF:

0.0000724

Gnomad4 OTH exome

AF:

0.0000882

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000304

AC:

AN:

131560

Hom.:

Cov.:

AF XY:

0.000464

AC XY:

AN XY:

62488

show subpopulations

Gnomad4 AFR

AF:

0.0000294

Gnomad4 AMR

AF:

0.0000803

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000216

Gnomad4 SAS

AF:

0.000282

Gnomad4 FIN

AF:

0.00377

Gnomad4 NFE

AF:

0.0000639

Gnomad4 OTH

AF:

0.000599

Alfa

AF:

0.000280

Hom.:

Bravo

AF:

0.000102

ExAC

AF:

0.0000931

AC:

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

Invitae

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.29

BayesDel_noAF

Pathogenic

0.55

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Uncertain

0.68

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.76

MutationTaster

Benign

1.0

A;A;A;A;A;A

Vest4

0.49

GERP RS

3.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: -24

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