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GeneBe

X-102937753-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001031834.1(RAB40AL):c.435C>T(p.Ala145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0412 in 1,197,623 control chromosomes in the GnomAD database, including 4,728 homozygotes. There are 19,394 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1517 hom., 2821 hem., cov: 22)
Exomes 𝑓: 0.034 ( 3211 hom. 16573 hem. )

Consequence

RAB40AL
NM_001031834.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.797
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 -15 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=-0.6).
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-102937753-C-T is Benign according to our data. Variant chrX-102937753-C-T is described in ClinVar as [Benign]. Clinvar id is 810918.Status of the report is criteria_provided_single_submitter, 1 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=-0.797 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 = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAB40ALNM_001031834.1 linkuse as main transcriptc.435C>T p.Ala145= synonymous_variant 1/1 ENST00000218249.7
LINC00630NR_146589.1 linkuse as main transcriptn.1910-20895C>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.435C>T p.Ala145= synonymous_variant 1/1 NM_001031834.1 P1
ENST00000413528.1 linkuse as main transcript downstream_gene_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
12392
AN:
109900
Hom.:
1514
Cov.:
22
AF XY:
0.0863
AC XY:
2806
AN XY:
32518
show subpopulations
Gnomad AFR
AF:
0.343
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0606
Gnomad ASJ
AF:
0.0128
Gnomad EAS
AF:
0.156
Gnomad SAS
AF:
0.298
Gnomad FIN
AF:
0.00571
Gnomad MID
AF:
0.0168
Gnomad NFE
AF:
0.00550
Gnomad OTH
AF:
0.0886
GnomAD3 exomes
AF:
0.0641
AC:
11329
AN:
176844
Hom.:
1120
AF XY:
0.0699
AC XY:
4610
AN XY:
65948
show subpopulations
Gnomad AFR exome
AF:
0.300
Gnomad AMR exome
AF:
0.0374
Gnomad ASJ exome
AF:
0.0112
Gnomad EAS exome
AF:
0.120
Gnomad SAS exome
AF:
0.288
Gnomad FIN exome
AF:
0.00584
Gnomad NFE exome
AF:
0.00359
Gnomad OTH exome
AF:
0.0390
GnomAD4 exome
AF:
0.0340
AC:
36962
AN:
1087678
Hom.:
3211
Cov.:
32
AF XY:
0.0458
AC XY:
16573
AN XY:
362236
show subpopulations
Gnomad4 AFR exome
AF:
0.356
Gnomad4 AMR exome
AF:
0.0449
Gnomad4 ASJ exome
AF:
0.0126
Gnomad4 EAS exome
AF:
0.168
Gnomad4 SAS exome
AF:
0.305
Gnomad4 FIN exome
AF:
0.00771
Gnomad4 NFE exome
AF:
0.00388
Gnomad4 OTH exome
AF:
0.0570
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
12412
AN:
109945
Hom.:
1517
Cov.:
22
AF XY:
0.0866
AC XY:
2821
AN XY:
32577
show subpopulations
Gnomad4 AFR
AF:
0.343
Gnomad4 AMR
AF:
0.0607
Gnomad4 ASJ
AF:
0.0128
Gnomad4 EAS
AF:
0.157
Gnomad4 SAS
AF:
0.294
Gnomad4 FIN
AF:
0.00571
Gnomad4 NFE
AF:
0.00550
Gnomad4 OTH
AF:
0.0941
Alfa
AF:
0.0601
Hom.:
488
Bravo
AF:
0.140

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 testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesSep 13, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
Cadd
Benign
0.0090
Dann
Benign
0.59

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: rs61745022; hg19: chrX-102192681; COSMIC: COSV54435048; COSMIC: COSV54435048; API