chr7-38726749-C-T

Position:

• chr7-38726749-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014396.4(VPS41):​c.2484+160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,236 control chromosomes in the GnomAD database, including 639 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.086 (639 hom., cov: 33)
• Consequence: VPS41 NM_014396.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.244

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 7-38726749-C-T is Benign according to our data. Variant chr7-38726749-C-T is described in ClinVar as [Benign]. Clinvar id is 1279808.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	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS41	NM_014396.4	c.2484+160G>A		intron_variant		ENST00000310301.9
VPS41	NM_080631.4	c.2409+160G>A		intron_variant
VPS41	XM_017011988.2	c.1329+160G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS41	ENST00000310301.9	c.2484+160G>A		intron_variant		1	NM_014396.4	P1

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13112 AN: 152118 Hom.: 636 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0746

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0863 AC: 13135 AN: 152236 Hom.: 639 Cov.: 33 AF XY: 0.0860 AC XY: 6405 AN XY: 74460

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0593

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.00501

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0841

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0936 Hom.: 112

Bravo AF: 0.0809

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.79
CADD	Benign	4.2
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs13224857; hg19: chr7-38766349;