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X-102937765-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.447C>T(p.Gly149=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 1,195,088 control chromosomes in the GnomAD database, including 5,304 homozygotes. There are 20,393 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1749 hom., 3133 hem., cov: 21)
Exomes 𝑓: 0.035 ( 3555 hom. 17260 hem. )

Consequence

RAB40AL
NM_001031834.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.421
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=-0.55).
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-102937765-C-T is Benign according to our data. Variant chrX-102937765-C-T is described in ClinVar as [Benign]. Clinvar id is 810919.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=0.421 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 = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAB40ALNM_001031834.1 linkuse as main transcriptc.447C>T p.Gly149= synonymous_variant 1/1 ENST00000218249.7
LINC00630NR_146589.1 linkuse as main transcriptn.1910-20883C>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.447C>T p.Gly149= 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:
0.120
AC:
13216
AN:
109729
Hom.:
1745
Cov.:
21
AF XY:
0.0954
AC XY:
3113
AN XY:
32629
show subpopulations
Gnomad AFR
AF:
0.364
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0625
Gnomad ASJ
AF:
0.0129
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.301
Gnomad FIN
AF:
0.00536
Gnomad MID
AF:
0.0169
Gnomad NFE
AF:
0.00556
Gnomad OTH
AF:
0.0910
GnomAD3 exomes
AF:
0.0679
AC:
12010
AN:
176889
Hom.:
1293
AF XY:
0.0735
AC XY:
4846
AN XY:
65941
show subpopulations
Gnomad AFR exome
AF:
0.325
Gnomad AMR exome
AF:
0.0384
Gnomad ASJ exome
AF:
0.0109
Gnomad EAS exome
AF:
0.144
Gnomad SAS exome
AF:
0.288
Gnomad FIN exome
AF:
0.00577
Gnomad NFE exome
AF:
0.00363
Gnomad OTH exome
AF:
0.0406
GnomAD4 exome
AF:
0.0352
AC:
38235
AN:
1085305
Hom.:
3555
Cov.:
32
AF XY:
0.0478
AC XY:
17260
AN XY:
361401
show subpopulations
Gnomad4 AFR exome
AF:
0.379
Gnomad4 AMR exome
AF:
0.0460
Gnomad4 ASJ exome
AF:
0.0124
Gnomad4 EAS exome
AF:
0.188
Gnomad4 SAS exome
AF:
0.306
Gnomad4 FIN exome
AF:
0.00772
Gnomad4 NFE exome
AF:
0.00396
Gnomad4 OTH exome
AF:
0.0595
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.121
AC:
13242
AN:
109783
Hom.:
1749
Cov.:
21
AF XY:
0.0958
AC XY:
3133
AN XY:
32693
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.0625
Gnomad4 ASJ
AF:
0.0129
Gnomad4 EAS
AF:
0.191
Gnomad4 SAS
AF:
0.296
Gnomad4 FIN
AF:
0.00536
Gnomad4 NFE
AF:
0.00556
Gnomad4 OTH
AF:
0.0959
Alfa
AF:
0.0621
Hom.:
509
Bravo
AF:
0.144

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
-0.55
Cadd
Benign
0.076
Dann
Benign
0.49

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: rs7066794; hg19: chrX-102192693; COSMIC: COSV54434660; COSMIC: COSV54434660; API