9-77238164-T-G

Position:

• chr9-77238164-T-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_033305.3(VPS13A):​c.1758T>G​(p.Ala586=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A586A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: VPS13A NM_033305.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

Genes affected

VPS13A (HGNC:1908): (vacuolar protein sorting 13 homolog A) The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP7: Synonymous conserved (PhyloP=0.244 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VPS13A	NM_033305.3	c.1758T>G	p.Ala586=	synonymous_variant	18/72	ENST00000360280.8	NP_150648.2
VPS13A	NM_001018037.2	c.1758T>G	p.Ala586=	synonymous_variant	18/71		NP_001018047.1
VPS13A	NM_015186.4	c.1758T>G	p.Ala586=	synonymous_variant	18/69		NP_056001.1
VPS13A	NM_001018038.3	c.1758T>G	p.Ala586=	synonymous_variant	18/69		NP_001018048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VPS13A	ENST00000360280.8	c.1758T>G	p.Ala586=	synonymous_variant	18/72	1	NM_033305.3	ENSP00000353422	P4
VPS13A	ENST00000376636.7	c.1758T>G	p.Ala586=	synonymous_variant	18/71	1		ENSP00000365823
VPS13A	ENST00000643348.1	c.1758T>G	p.Ala586=	synonymous_variant	18/69			ENSP00000493592
VPS13A	ENST00000645632.1	c.1758T>G	p.Ala586=	synonymous_variant	18/69			ENSP00000496361	A1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.6
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs149037185; hg19: chr9-79853080;