Variant rs34835605 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001193315.2(VIPAS39):c.1179+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,612,142 control chromosomes in the GnomAD database, including 29,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2248 hom., cov: 32)

Exomes 𝑓: 0.19 ( 27275 hom. )

Consequence

VIPAS39
NM_001193315.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.10

Variant links:

Genes affected

VIPAS39 (HGNC:20347): (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog) Involved in endosome to lysosome transport and intracellular protein transport. Acts upstream of or within collagen metabolic process and peptidyl-lysine hydroxylation. Located in Golgi apparatus and endosome. Implicated in arthrogryposis, renal dysfunction, and cholestasis 2. [provided by Alliance of Genome Resources, Apr 2022]

VIPAS39 links:

VIPAS39 (HGNC:):

VIPAS39 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 14-77433822-C-T is Benign according to our data. Variant chr14-77433822-C-T is described in ClinVar as [Benign]. Clinvar id is 261486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VIPAS39	NM_001193315.2 linkuse as main transcript	c.1179+20G>A		intron_variant		ENST00000557658.6	NP_001180244.1	Q9H9C1-1Q6IA61

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VIPAS39	ENST00000557658.6 linkuse as main transcript	c.1179+20G>A		intron_variant		1	NM_001193315.2	ENSP00000452191.1		Q9H9C1-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23844

AN:

151986

Hom.:

2246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0807

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0166

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.175

GnomAD3 exomes

AF:

0.186

AC:

46564

AN:

250862

Hom.:

4987

AF XY:

0.189

AC XY:

25624

AN XY:

135568

show subpopulations

Gnomad AFR exome

AF:

0.0791

Gnomad AMR exome

AF:

0.287

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.00914

Gnomad SAS exome

AF:

0.250

Gnomad FIN exome

AF:

0.162

Gnomad NFE exome

AF:

0.188

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.188

AC:

273988

AN:

1460038

Hom.:

27275

Cov.:

AF XY:

0.190

AC XY:

137754

AN XY:

726440

show subpopulations

Gnomad4 AFR exome

AF:

0.0759

Gnomad4 AMR exome

AF:

0.277

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.00800

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.157

AC:

23858

AN:

152104

Hom.:

2248

Cov.:

AF XY:

0.157

AC XY:

11680

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0806

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.0164

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.169

Hom.:

396

Bravo

AF:

0.160

Asia WGS

AF:

0.126

AC:

441

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 02, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.26

DANN

Benign

0.45

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