chr9-77177159-G-C

Variant names:

• chr9-77177159-G-C
• rs12349251
• ENST00000644612.2:n.576-253C>G

Variant summary

Our verdict is Benign. The variant received -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 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.667
• Publications: 2 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=-0.81).
• 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 rank	MANE	Protein	UniProt
VPS13A-AS1	NR_026668.2	n.292-253C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VPS13A-AS1	ENST00000644612.2	n.576-253C>G		intron_variant	Intron 1 of 1
VPS13A-AS1	ENST00000721227.1	n.267-273C>G		intron_variant	Intron 1 of 1
VPS13A-AS1	ENST00000721228.1	n.290+66C>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.111 AC: 4591 AN: 41546

American (AMR) AF: 0.0746 AC: 1141 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3468

East Asian (EAS) AF: 0.0368 AC: 190 AN: 5166

South Asian (SAS) AF: 0.0754 AC: 364 AN: 4830

European-Finnish (FIN) AF: 0.124 AC: 1315 AN: 10606

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7321 AN: 67986

Other (OTH) AF: 0.0941 AC: 199 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	-0.81
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.67
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12349251; hg19: chr9-79792075;