Variant X-102937753-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

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

Clinical Significance

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

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]

RAB40AL links:

LINC00630 (HGNC:):

LINC00630 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

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_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.797 with no splicing effect.

BA1

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	Protein	UniProt
RAB40AL	NM_001031834.1 linkuse as main transcript	c.435C>T	p.Ala145=	synonymous_variant	1/1	ENST00000218249.7	NP_001027004.1
LINC00630	NR_146589.1 linkuse as main transcript	n.1910-20895C>T		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.435C>T	p.Ala145=	synonymous_variant	1/1		NM_001031834.1	ENSP00000218249	P1
	ENST00000413528.1 linkuse as main transcript			downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

12392

AN:

109900

Hom.:

1514

Cov.:

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.:

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

AF:

0.113

AC:

12412

AN:

109945

Hom.:

1517

Cov.:

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: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

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.

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