Variant 17-82657906-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_006822.3(RAB40B):c.794G>A(p.Ser265Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000335 in 1,311,792 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 24)

Exomes 𝑓: 0.000034 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RAB40B
NM_006822.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.82

Variant links:

Genes affected

RAB40B (HGNC:18284): (RAB40B, member RAS oncogene family) The protein encoded by this gene has similarity to a yeast protein which suggests a role of the gene product in regulating secretory vesicles. [provided by RefSeq, Jul 2008]

RAB40B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB40B	NM_006822.3 linkuse as main transcript	c.794G>A	p.Ser265Asn	missense_variant	6/6	ENST00000571995.6	NP_006813.1	Q12829
RAB40B	XM_011523528.3 linkuse as main transcript	c.743G>A	p.Ser248Asn	missense_variant	6/6		XP_011521830.1
RAB40B	XM_006722271.4 linkuse as main transcript	c.674G>A	p.Ser225Asn	missense_variant	6/6		XP_006722334.1
RAB40B	XM_017024042.2 linkuse as main transcript	c.614G>A	p.Ser205Asn	missense_variant	6/6		XP_016879531.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB40B	ENST00000571995.6 linkuse as main transcript	c.794G>A	p.Ser265Asn	missense_variant	6/6	1	NM_006822.3	ENSP00000461785.1		Q12829

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

114184

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000282

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000299

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00141

Gnomad SAS

AF:

0.000569

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000537

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000335

AC:

AN:

1311792

Hom.:

Cov.:

AF XY:

0.0000306

AC XY:

AN XY:

652838

show subpopulations

Gnomad4 AFR exome

AF:

0.0000991

Gnomad4 AMR exome

AF:

0.000272

Gnomad4 ASJ exome

AF:

0.000167

Gnomad4 EAS exome

AF:

0.000236

Gnomad4 SAS exome

AF:

0.0000135

Gnomad4 FIN exome

AF:

0.0000400

Gnomad4 NFE exome

AF:

0.0000111

Gnomad4 OTH exome

AF:

0.0000552

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000193

AC:

AN:

114184

Hom.:

Cov.:

AF XY:

0.000185

AC XY:

AN XY:

54174

show subpopulations

Gnomad4 AFR

AF:

0.000281

Gnomad4 AMR

AF:

0.000299

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00141

Gnomad4 SAS

AF:

0.000572

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000537

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 10, 2021

The c.794G>A (p.S265N) alteration is located in exon 6 (coding exon 6) of the RAB40B gene. This alteration results from a G to A substitution at nucleotide position 794, causing the serine (S) at amino acid position 265 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.032

BayesDel_noAF

Benign

-0.28

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0072

T;.

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.56

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.90

D;D

M_CAP

Benign

0.076

MetaRNN

Uncertain

0.55

D;D

MetaSVM

Benign

-0.28

MutationAssessor

Uncertain

2.0

M;.

PrimateAI

Benign

0.41

REVEL

Benign

0.16

Sift4G

Uncertain

0.040

D;D

Polyphen

0.90

P;.

Vest4

0.55

MVP

0.90

MPC

1.2

ClinPred

0.68

GERP RS

4.8

Varity_R

0.35

gMVP

0.53

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