11-65096497-TG-T

Position:

• chr11-65096497-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_013265.4(VPS51):​c.228+26del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (13479 hom., cov: 0)
  • Exomes 𝑓: 0.55 (61693 hom.)
  • Failed GnomAD Quality Control
• Consequence: VPS51 NM_013265.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.257

Genes affected

VPS51 (HGNC:1172): (VPS51 subunit of GARP complex) This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the early and late endosomes to the trans-Golgi network. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-65096497-TG-T is Benign according to our data. Variant chr11-65096497-TG-T is described in ClinVar as [Benign]. Clinvar id is 1262736.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VPS51	NM_013265.4	c.228+26del		intron_variant		ENST00000279281.8	NP_037397.2
VPS51	NR_073519.2	n.265+26del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VPS51	ENST00000279281.8	c.228+26del		intron_variant		1	NM_013265.4	ENSP00000279281	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 63752 AN: 107418 Hom.: 13440 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.581

GnomAD3 exomes AF: 0.463 AC: 32236 AN: 69632 Hom.: 6912 AF XY: 0.458 AC XY: 18130 AN XY: 39568

Gnomad AFR exome AF: 0.492

Gnomad AMR exome AF: 0.596

Gnomad ASJ exome AF: 0.483

Gnomad EAS exome AF: 0.323

Gnomad SAS exome AF: 0.385

Gnomad FIN exome AF: 0.477

Gnomad NFE exome AF: 0.478

Gnomad OTH exome AF: 0.509

GnomAD4 exome AF: 0.555 AC: 288126 AN: 519610 Hom.: 61693 Cov.: 0 AF XY: 0.550 AC XY: 147128 AN XY: 267562

Gnomad4 AFR exome AF: 0.552

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.528

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.469

Gnomad4 FIN exome AF: 0.525

Gnomad4 NFE exome AF: 0.577

Gnomad4 OTH exome AF: 0.562

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.594 AC: 63844 AN: 107532 Hom.: 13479 Cov.: 0 AF XY: 0.594 AC XY: 30969 AN XY: 52130

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.580

Asia WGS AF: 0.327 AC: 1133 AN: 3466

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

Aug 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs61505294; hg19: chr11-64863969;