Variant chr7-38742250-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014396.4(VPS41):c.2123-129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 880,614 control chromosomes in the GnomAD database, including 2,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 419 hom., cov: 33)

Exomes 𝑓: 0.077 ( 2527 hom. )

Consequence

VPS41
NM_014396.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.559

Variant links:

Genes affected

VPS41 (HGNC:12713): (VPS41 subunit of HOPS complex) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]

VPS41 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 7-38742250-T-C is Benign according to our data. Variant chr7-38742250-T-C is described in ClinVar as [Benign]. Clinvar id is 1273716.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
VPS41	NM_014396.4 linkuse as main transcript	c.2123-129A>G	intron_variant	ENST00000310301.9
VPS41	NM_080631.4 linkuse as main transcript	c.2048-129A>G	intron_variant
VPS41	XM_017011988.2 linkuse as main transcript	c.968-129A>G	intron_variant
VPS41	XR_007060008.1 linkuse as main transcript	n.2140-129A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS41	ENST00000310301.9 linkuse as main transcript	c.2123-129A>G		intron_variant		1	NM_014396.4	P1	P49754-1

Frequencies

GnomAD3 genomes

AF:

0.0608

AC:

9250

AN:

152170

Hom.:

420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0129

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.0479

Gnomad ASJ

AF:

0.0744

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.0846

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0878

Gnomad OTH

AF:

0.0502

GnomAD4 exome

AF:

0.0771

AC:

56181

AN:

728326

Hom.:

2527

AF XY:

0.0794

AC XY:

29528

AN XY:

371772

show subpopulations

Gnomad4 AFR exome

AF:

0.0110

Gnomad4 AMR exome

AF:

0.0349

Gnomad4 ASJ exome

AF:

0.0734

Gnomad4 EAS exome

AF:

0.000961

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.0902

Gnomad4 NFE exome

AF:

0.0795

Gnomad4 OTH exome

AF:

0.0750

GnomAD4 genome

AF:

0.0608

AC:

9253

AN:

152288

Hom.:

419

Cov.:

AF XY:

0.0607

AC XY:

4519

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0129

Gnomad4 AMR

AF:

0.0479

Gnomad4 ASJ

AF:

0.0744

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.0846

Gnomad4 NFE

AF:

0.0878

Gnomad4 OTH

AF:

0.0511

Alfa

AF:

0.0814

Hom.:

Bravo

AF:

0.0518

Asia WGS

AF:

0.0590

AC:

205

AN:

3474

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 submitter

clinical testing

GeneDx

May 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.87

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