ENST00000644612.2:n.576-197G>C

Variant names:

• chr9-77177103-C-G
• rs12340377
• ENST00000644612.2:n.576-197G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000644612.2(VPS13A-AS1):​n.576-197G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,134 control chromosomes in the GnomAD database, including 819 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (819 hom., cov: 32)
• Consequence: VPS13A-AS1 ENST00000644612.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0750
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 9-77177103-C-G is Benign according to our data. Variant chr9-77177103-C-G is described in ClinVar as [Benign]. Clinvar id is 1249099.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VPS13A-AS1	NR_026668.2	n.292-197G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VPS13A-AS1	ENST00000644612.2	n.576-197G>C		intron_variant	Intron 1 of 1
VPS13A-AS1	ENST00000721227.1	n.267-217G>C		intron_variant	Intron 1 of 1
VPS13A-AS1	ENST00000721228.1	n.290+122G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15543 AN: 152016 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.102 AC: 15557 AN: 152134 Hom.: 819 Cov.: 32 AF XY: 0.101 AC XY: 7521 AN XY: 74368

African (AFR) AF: 0.110 AC: 4569 AN: 41502

American (AMR) AF: 0.0744 AC: 1139 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3466

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5176

South Asian (SAS) AF: 0.0747 AC: 360 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7304 AN: 67942

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

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

Jul 17, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.46
PhyloP100		-0.075
PromoterAI		0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12340377; hg19: chr9-79792019;