rs9784907

chr7-93317144-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017667.4(VPS50):c.1855+5872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,148 control chromosomes in the GnomAD database, including 12,290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (12290 hom., cov: 32)
• Consequence: VPS50 NM_017667.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

VPS50 (HGNC:25956): (VPS50 subunit of EARP/GARPII complex) Enables SNARE binding activity. Acts upstream of or within endocytic recycling. Located in recycling endosome. Part of EARP complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS50	NM_017667.4	c.1855+5872A>G		intron_variant		ENST00000305866.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS50	ENST00000305866.10	c.1855+5872A>G		intron_variant		1	NM_017667.4	P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46474 AN: 152030 Hom.: 12269 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.306 AC: 46550 AN: 152148 Hom.: 12290 Cov.: 32 AF XY: 0.299 AC XY: 22270 AN XY: 74396

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.254

Alfa AF: 0.185 Hom.: 2854

Bravo AF: 0.323

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.64
Dann	Benign	0.48

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: rs9784907; hg19: chr7-92946456;