Variant 9-77177270-T-TG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NR_026668.2(VPS13A-AS1):n.291+356_291+357insC variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00802 in 193,280 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0077 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 2 hom. )

Consequence

VPS13A-AS1
NR_026668.2 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.783

Variant links:

Genes affected

VPS13A-AS1 (HGNC:44167): (VPS13A antisense RNA 1)

VPS13A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-77177270-T-TG is Benign according to our data. Variant chr9-77177270-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 1703371.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00907 (373/41140) while in subpopulation MID AF= 0.0357 (6/168). AF 95% confidence interval is 0.0156. There are 2 homozygotes in gnomad4_exome. There are 171 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS13A-AS1	NR_026668.2 linkuse as main transcript	n.291+356_291+357insC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS13A-AS1	ENST00000644612.1 linkuse as main transcript	n.554+356_554+357insC		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00776

AC:

1179

AN:

152022

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00251

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.00530

Gnomad ASJ

AF:

0.0184

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.0605

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.00862

GnomAD4 exome

AF:

0.00907

AC:

373

AN:

41140

Hom.:

AF XY:

0.00793

AC XY:

171

AN XY:

21564

show subpopulations

Gnomad4 AFR exome

AF:

0.00568

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.0138

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00186

Gnomad4 FIN exome

AF:

0.00363

Gnomad4 NFE exome

AF:

0.0111

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.00774

AC:

1178

AN:

152140

Hom.:

Cov.:

AF XY:

0.00730

AC XY:

543

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.00250

Gnomad4 AMR

AF:

0.00529

Gnomad4 ASJ

AF:

0.0184

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00291

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.00853

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.00830

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 16, 2020

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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