Variant 22-50769034-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001130919.3(RABL2B):c.591+7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 70 hom., cov: 19)

Exomes 𝑓: 0.0041 ( 74 hom. )

Consequence

RABL2B
NM_001130919.3 splice_region, intron

Scores

Splicing: ADA: 0.00009740

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.343

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 22-50769034-G-T is Benign according to our data. Variant chr22-50769034-G-T is described in ClinVar as [Benign]. Clinvar id is 769168.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RABL2B	NM_001130919.3 linkuse as main transcript	c.591+7C>A		splice_region_variant, intron_variant		ENST00000691320.1
RPL23AP82	NR_026981.1 linkuse as main transcript	n.241+11708G>T		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.591+7C>A		splice_region_variant, intron_variant			NM_001130919.3	A2	Q9UNT1-2
RPL23AP7	ENST00000496652.5 linkuse as main transcript	n.379+11708G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0179

AC:

2419

AN:

134962

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0556

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0175

Gnomad ASJ

AF:

0.0161

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000799

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0292

Gnomad NFE

AF:

0.00211

Gnomad OTH

AF:

0.0271

GnomAD3 exomes

AF:

0.00834

AC:

783

AN:

93864

Hom.:

AF XY:

0.00764

AC XY:

363

AN XY:

47518

show subpopulations

Gnomad AFR exome

AF:

0.0680

Gnomad AMR exome

AF:

0.00938

Gnomad ASJ exome

AF:

0.0124

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000452

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00290

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.00411

AC:

4339

AN:

1055782

Hom.:

Cov.:

AF XY:

0.00392

AC XY:

2063

AN XY:

526104

show subpopulations

Gnomad4 AFR exome

AF:

0.0641

Gnomad4 AMR exome

AF:

0.00996

Gnomad4 ASJ exome

AF:

0.0123

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000467

Gnomad4 FIN exome

AF:

0.0000216

Gnomad4 NFE exome

AF:

0.00204

Gnomad4 OTH exome

AF:

0.0100

GnomAD4 genome

AF:

0.0181

AC:

2443

AN:

135062

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1151

AN XY:

64446

show subpopulations

Gnomad4 AFR

AF:

0.0562

Gnomad4 AMR

AF:

0.0174

Gnomad4 ASJ

AF:

0.0161

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000534

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00207

Gnomad4 OTH

AF:

0.0269

Alfa

AF:

0.0112

Hom.:

Bravo

AF:

0.0228

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000097

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.54

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.54

Position offset: 3

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