Variant X-102937333-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001031834.1(RAB40AL):c.15C>T(p.Gly5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00703 in 1,209,679 control chromosomes in the GnomAD database, including 33 homozygotes. There are 2,680 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0044 ( 0 hom., 132 hem., cov: 23)

Exomes 𝑓: 0.0073 ( 33 hom. 2548 hem. )

Consequence

RAB40AL
NM_001031834.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.145

Variant links:

Genes affected

RAB40AL (HGNC:25410): (RAB40A like) This gene encodes a member of the Rab40 subfamily of Rab small GTP-binding proteins that contains a C-terminal suppressors of cytokine signaling box. Disruptions in this gene are associated with Duchenne muscular dystrophy. [provided by RefSeq, Apr 2010]

RAB40AL links:

LINC00630 (HGNC:):

LINC00630 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant X-102937333-C-T is Benign according to our data. Variant chrX-102937333-C-T is described in ClinVar as [Benign]. Clinvar id is 780080.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-102937333-C-T is described in Lovd as [Benign]. Variant chrX-102937333-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.145 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 132 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB40AL	NM_001031834.1 linkuse as main transcript	c.15C>T	p.Gly5=	synonymous_variant	1/1	ENST00000218249.7	NP_001027004.1
LINC00630	NR_146589.1 linkuse as main transcript	n.1910-21315C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB40AL	ENST00000218249.7 linkuse as main transcript	c.15C>T	p.Gly5=	synonymous_variant	1/1		NM_001031834.1	ENSP00000218249	P1

Frequencies

GnomAD3 genomes

AF:

0.00439

AC:

494

AN:

112420

Hom.:

Cov.:

AF XY:

0.00385

AC XY:

133

AN XY:

34552

show subpopulations

Gnomad AFR

AF:

0.00175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00168

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000737

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00768

Gnomad OTH

AF:

0.00724

GnomAD3 exomes

AF:

0.00358

AC:

649

AN:

181217

Hom.:

AF XY:

0.00352

AC XY:

232

AN XY:

65977

show subpopulations

Gnomad AFR exome

AF:

0.00131

Gnomad AMR exome

AF:

0.00179

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000855

Gnomad FIN exome

AF:

0.000506

Gnomad NFE exome

AF:

0.00664

Gnomad OTH exome

AF:

0.00515

GnomAD4 exome

AF:

0.00730

AC:

8012

AN:

1097206

Hom.:

Cov.:

AF XY:

0.00702

AC XY:

2548

AN XY:

362720

show subpopulations

Gnomad4 AFR exome

AF:

0.000796

Gnomad4 AMR exome

AF:

0.00199

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000611

Gnomad4 FIN exome

AF:

0.000594

Gnomad4 NFE exome

AF:

0.00897

Gnomad4 OTH exome

AF:

0.00654

GnomAD4 genome

AF:

0.00438

AC:

493

AN:

112473

Hom.:

Cov.:

AF XY:

0.00381

AC XY:

132

AN XY:

34615

show subpopulations

Gnomad4 AFR

AF:

0.00174

Gnomad4 AMR

AF:

0.00168

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000740

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00766

Gnomad4 OTH

AF:

0.00715

Alfa

AF:

0.00379

Hom.:

Bravo

AF:

0.00406

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 06, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

3.6

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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