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GeneBe

X-102937444-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001031834.1(RAB40AL):c.126G>A(p.Pro42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,210,026 control chromosomes in the GnomAD database, including 72 homozygotes. There are 894 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 38 hom., 424 hem., cov: 22)
Exomes 𝑓: 0.0016 ( 34 hom. 470 hem. )

Consequence

RAB40AL
NM_001031834.1 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -1.08
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-102937444-G-A is Benign according to our data. Variant chrX-102937444-G-A is described in ClinVar as [Benign]. Clinvar id is 618338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAB40ALNM_001031834.1 linkuse as main transcriptc.126G>A p.Pro42= synonymous_variant 1/1 ENST00000218249.7
LINC00630NR_146589.1 linkuse as main transcriptn.1910-21204G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAB40ALENST00000218249.7 linkuse as main transcriptc.126G>A p.Pro42= synonymous_variant 1/1 NM_001031834.1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0150
AC:
1671
AN:
111745
Hom.:
38
Cov.:
22
AF XY:
0.0125
AC XY:
424
AN XY:
33929
show subpopulations
Gnomad AFR
AF:
0.0523
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00451
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000750
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000565
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00461
AC:
846
AN:
183502
Hom.:
19
AF XY:
0.00289
AC XY:
196
AN XY:
67930
show subpopulations
Gnomad AFR exome
AF:
0.0597
Gnomad AMR exome
AF:
0.00160
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000722
Gnomad SAS exome
AF:
0.000315
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000244
Gnomad OTH exome
AF:
0.00177
GnomAD4 exome
AF:
0.00161
AC:
1768
AN:
1098230
Hom.:
34
Cov.:
32
AF XY:
0.00129
AC XY:
470
AN XY:
363586
show subpopulations
Gnomad4 AFR exome
AF:
0.0570
Gnomad4 AMR exome
AF:
0.00193
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000332
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000166
Gnomad4 OTH exome
AF:
0.00349
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0150
AC:
1672
AN:
111796
Hom.:
38
Cov.:
22
AF XY:
0.0125
AC XY:
424
AN XY:
33990
show subpopulations
Gnomad4 AFR
AF:
0.0522
Gnomad4 AMR
AF:
0.00450
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000752
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000565
Gnomad4 OTH
AF:
0.0119
Alfa
AF:
0.00866
Hom.:
36
Bravo
AF:
0.0180
EpiCase
AF:
0.000164
EpiControl
AF:
0.000119

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 submitterclinical testingInvitaeFeb 25, 2018- -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesDec 22, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
0.67
Dann
Benign
0.77

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.

Other links and lift over

dbSNP: rs61745023; hg19: chrX-102192372; COSMIC: COSV54434032; COSMIC: COSV54434032; API