Variant chr7-38726125-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_014396.4(VPS41):c.*121A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 680,930 control chromosomes in the GnomAD database, including 137 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 53 hom., cov: 33)

Exomes 𝑓: 0.013 ( 84 hom. )

Consequence

VPS41
NM_014396.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.437

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=-0.84).

BP6

Variant 7-38726125-T-C is Benign according to our data. Variant chr7-38726125-T-C is described in ClinVar as [Benign]. Clinvar id is 1285662.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0231 (3510/152228) while in subpopulation AFR AF= 0.0485 (2016/41546). AF 95% confidence interval is 0.0468. There are 53 homozygotes in gnomad4. There are 1630 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 53 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
VPS41	NM_014396.4 linkuse as main transcript	c.*121A>G	3_prime_UTR_variant	29/29	ENST00000310301.9
VPS41	NM_080631.4 linkuse as main transcript	c.*121A>G	3_prime_UTR_variant	28/28
VPS41	XM_017011988.2 linkuse as main transcript	c.*121A>G	3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS41	ENST00000310301.9 linkuse as main transcript	c.*121A>G	3_prime_UTR_variant	29/29	1	NM_014396.4	P1	P49754-1
VPS41	ENST00000395969.6 linkuse as main transcript	c.*121A>G	3_prime_UTR_variant	28/28	5			P49754-3
VPS41	ENST00000490924.1 linkuse as main transcript	n.480A>G	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.0231

AC:

3508

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0486

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0141

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00976

Gnomad FIN

AF:

0.00727

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0186

GnomAD4 exome

AF:

0.0131

AC:

6948

AN:

528702

Hom.:

Cov.:

AF XY:

0.0125

AC XY:

3512

AN XY:

280080

show subpopulations

Gnomad4 AFR exome

AF:

0.0506

Gnomad4 AMR exome

AF:

0.00974

Gnomad4 ASJ exome

AF:

0.00170

Gnomad4 EAS exome

AF:

0.000285

Gnomad4 SAS exome

AF:

0.00798

Gnomad4 FIN exome

AF:

0.00901

Gnomad4 NFE exome

AF:

0.0148

Gnomad4 OTH exome

AF:

0.0151

GnomAD4 genome

AF:

0.0231

AC:

3510

AN:

152228

Hom.:

Cov.:

AF XY:

0.0219

AC XY:

1630

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0485

Gnomad4 AMR

AF:

0.0141

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00956

Gnomad4 FIN

AF:

0.00727

Gnomad4 NFE

AF:

0.0152

Gnomad4 OTH

AF:

0.0184

Alfa

AF:

0.0186

Hom.:

Bravo

AF:

0.0247

Asia WGS

AF:

0.00751

AC:

AN:

3478

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 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.80

DANN

Benign

0.62

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