Variant chrX-102937400-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001031834.1(RAB40AL):c.82A>G(p.Ser28Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 111,147 control chromosomes in the GnomAD database, including 2,621 homozygotes. There are 4,849 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2621 hom., 4849 hem., cov: 22)

Exomes 𝑓: 0.042 ( 4473 hom. 18593 hem. )

Failed GnomAD Quality Control

Consequence

RAB40AL
NM_001031834.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.40

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.554259E-4).

BP6

Variant X-102937400-A-G is Benign according to our data. Variant chrX-102937400-A-G is described in ClinVar as [Benign]. Clinvar id is 810917.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB40AL	NM_001031834.1 linkuse as main transcript	c.82A>G	p.Ser28Gly	missense_variant	1/1	ENST00000218249.7	NP_001027004.1
LINC00630	NR_146589.1 linkuse as main transcript	n.1910-21248A>G		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.82A>G	p.Ser28Gly	missense_variant	1/1		NM_001031834.1	ENSP00000218249	P1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

17059

AN:

111096

Hom.:

2617

Cov.:

AF XY:

0.145

AC XY:

4827

AN XY:

33358

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0765

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.00671

Gnomad MID

AF:

0.0167

Gnomad NFE

AF:

0.00604

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.0860

AC:

15510

AN:

180345

Hom.:

1749

AF XY:

0.0900

AC XY:

6042

AN XY:

67165

show subpopulations

Gnomad AFR exome

AF:

0.471

Gnomad AMR exome

AF:

0.0478

Gnomad ASJ exome

AF:

0.0135

Gnomad EAS exome

AF:

0.145

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.00732

Gnomad NFE exome

AF:

0.00456

Gnomad OTH exome

AF:

0.0487

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0424

AC:

46580

AN:

1097888

Hom.:

4473

Cov.:

AF XY:

0.0512

AC XY:

18593

AN XY:

363436

show subpopulations

Gnomad4 AFR exome

AF:

0.492

Gnomad4 AMR exome

AF:

0.0611

Gnomad4 ASJ exome

AF:

0.0143

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.322

Gnomad4 FIN exome

AF:

0.00859

Gnomad4 NFE exome

AF:

0.00523

Gnomad4 OTH exome

AF:

0.0741

GnomAD4 genome

AF:

0.154

AC:

17089

AN:

111147

Hom.:

2621

Cov.:

AF XY:

0.145

AC XY:

4849

AN XY:

33419

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.0764

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.341

Gnomad4 FIN

AF:

0.00671

Gnomad4 NFE

AF:

0.00604

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.0621

Hom.:

549

Bravo

AF:

0.173

ESP6500AA

AF:

0.348

AC:

1332

ESP6500EA

AF:

0.00357

AC:

ExAC

AF:

0.102

AC:

12382

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 13, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.053

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.47

CADD

Benign

0.29

DANN

Benign

0.69

DEOGEN2

Benign

0.35

FATHMM_MKL

Benign

0.0077

LIST_S2

Benign

0.48

MetaRNN

Benign

0.00056

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.9

MutationTaster

Benign

1.0

PrimateAI

Benign

0.35

PROVEAN

Benign

0.41

REVEL

Uncertain

0.30

Sift

Benign

1.0

Sift4G

Benign

0.61

Polyphen

0.0

Vest4

0.061

MPC

0.40

ClinPred

0.025

GERP RS

0.99

Varity_R

0.046

gMVP

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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