Variant chr15-61854770-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020821.3(VPS13C):c.11160+101A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,169,994 control chromosomes in the GnomAD database, including 174,526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22378 hom., cov: 31)

Exomes 𝑓: 0.54 ( 152148 hom. )

Consequence

VPS13C
NM_020821.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.128

Variant links:

Genes affected

VPS13C (HGNC:23594): (vacuolar protein sorting 13 homolog C) Involved in mitochondrion organization and negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization. Located in cytosol and mitochondrial outer membrane. Implicated in Parkinson's disease 23. [provided by Alliance of Genome Resources, Apr 2022]

VPS13C links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 15-61854770-T-A is Benign according to our data. Variant chr15-61854770-T-A is described in ClinVar as [Benign]. Clinvar id is 1241074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
VPS13C	NM_020821.3 linkuse as main transcript	c.11160+101A>T	intron_variant	ENST00000644861.2
LOC124903501	XR_007064668.1 linkuse as main transcript	n.159+5298T>A	intron_variant, non_coding_transcript_variant
VPS13C	NM_017684.5 linkuse as main transcript	c.11031+101A>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS13C	ENST00000644861.2 linkuse as main transcript	c.11160+101A>T		intron_variant			NM_020821.3	P3	Q709C8-1
	ENST00000642740.1 linkuse as main transcript	n.172+5298T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81802

AN:

151806

Hom.:

22352

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.478

Gnomad FIN

AF:

0.712

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.532

GnomAD4 exome

AF:

0.544

AC:

553575

AN:

1018070

Hom.:

152148

AF XY:

0.541

AC XY:

277078

AN XY:

512586

show subpopulations

Gnomad4 AFR exome

AF:

0.499

Gnomad4 AMR exome

AF:

0.674

Gnomad4 ASJ exome

AF:

0.468

Gnomad4 EAS exome

AF:

0.487

Gnomad4 SAS exome

AF:

0.474

Gnomad4 FIN exome

AF:

0.716

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.526

GnomAD4 genome

AF:

0.539

AC:

81874

AN:

151924

Hom.:

22378

Cov.:

AF XY:

0.545

AC XY:

40438

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.495

Gnomad4 AMR

AF:

0.619

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.479

Gnomad4 FIN

AF:

0.712

Gnomad4 NFE

AF:

0.537

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.551

Hom.:

2800

Bravo

AF:

0.532

Asia WGS

AF:

0.482

AC:

1676

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.8

DANN

Benign

0.51

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