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GeneBe

X-102937333-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.51).
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-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_single_submitter, 1 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
?
    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=-0.145 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 133 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAB40ALNM_001031834.1 linkuse as main transcriptc.15C>T p.Gly5= synonymous_variant 1/1 ENST00000218249.7
LINC00630NR_146589.1 linkuse as main transcriptn.1910-21315C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAB40ALENST00000218249.7 linkuse as main transcriptc.15C>T p.Gly5= synonymous_variant 1/1 NM_001031834.1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00439
AC:
494
AN:
112420
Hom.:
0
Cov.:
23
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.:
0
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.:
33
Cov.:
31
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00438
AC:
493
AN:
112473
Hom.:
0
Cov.:
23
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.:
40
Bravo
AF:
0.00406

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 submitterclinical testingInvitaeApr 06, 2018- -

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.

Other links and lift over

dbSNP: rs5945909; hg19: chrX-102192261; API