Variant chrX-102937765-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.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

Clinical Significance

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

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]

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=-0.55).

BP6

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_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.421 with no splicing effect.

BA1

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	Protein	UniProt
RAB40AL	NM_001031834.1 linkuse as main transcript	c.447C>T	p.Gly149=	synonymous_variant	1/1	ENST00000218249.7	NP_001027004.1
LINC00630	NR_146589.1 linkuse as main transcript	n.1910-20883C>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.447C>T	p.Gly149=	synonymous_variant	1/1		NM_001031834.1	ENSP00000218249	P1
	ENST00000413528.1 linkuse as main transcript			downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

13216

AN:

109729

Hom.:

1745

Cov.:

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.:

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

AF:

0.121

AC:

13242

AN:

109783

Hom.:

1749

Cov.:

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: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

-0.55

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.

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