rs6132976

chr20-2844405-G-A

Variant summary

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

The NM_022575.4(VPS16):c.53+3578G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,190 control chromosomes in the GnomAD database, including 231 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 0.039 (231 hom., cov: 32)
• Consequence: VPS16 NM_022575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

Genes affected

VPS16 (HGNC:14584): (VPS16 core subunit of CORVET and HOPS complexes) 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 homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS16	NM_022575.4	c.53+3578G>A		intron_variant		ENST00000380445.8
VPS16	NM_080413.3	c.53+3578G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS16	ENST00000380445.8	c.53+3578G>A		intron_variant		1	NM_022575.4	P1
VPS16	ENST00000380469.7	c.53+3578G>A		intron_variant		2
VPS16	ENST00000417508.1	c.-75+3578G>A		intron_variant		5
VPS16	ENST00000453689.5	c.-75+3578G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5921 AN: 152074 Hom.: 221 Cov.: 32

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0391 AC: 5948 AN: 152190 Hom.: 231 Cov.: 32 AF XY: 0.0409 AC XY: 3046 AN XY: 74406

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0860

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0428 Hom.: 124

Bravo AF: 0.0474

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.7
Dann	Benign	0.77

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: rs6132976; hg19: chr20-2825051;