9-77177159-G-C

Position:

• chr9-77177159-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_026668.2(VPS13A-AS1):​n.292-253C>G 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 0.103 in 152,224 control chromosomes in the GnomAD database, including 830 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (830 hom., cov: 33)
• Consequence: VPS13A-AS1 NR_026668.2 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.667

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 9-77177159-G-C is Benign according to our data. Variant chr9-77177159-G-C is described in ClinVar as [Benign]. Clinvar id is 1257124.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VPS13A-AS1	NR_026668.2	n.292-253C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VPS13A-AS1	ENST00000644612.1	n.555-253C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15596 AN: 152106 Hom.: 830 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.103 AC: 15610 AN: 152224 Hom.: 830 Cov.: 33 AF XY: 0.101 AC XY: 7554 AN XY: 74426

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.0754

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0941

Alfa AF: 0.110 Hom.: 114

Bravo AF: 0.0992

Asia WGS AF: 0.0560 AC: 194 AN: 3478

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

Jul 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12349251; hg19: chr9-79792075;