chr6-142206005-A-G

Position:

• chr6-142206005-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016485.5(VTA1):​c.778+1940A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,172 control chromosomes in the GnomAD database, including 53,455 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53455 hom., cov: 32)
• Consequence: VTA1 NM_016485.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

VTA1 (HGNC:20954): (vesicle trafficking 1) C6ORF55 encodes a protein involved in trafficking of the multivesicular body, an endosomal compartment involved in sorting membrane proteins for degradation in lysosomes (Ward et al., 2005 [PubMed 15644320]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VTA1	NM_016485.5	c.778+1940A>G		intron_variant		ENST00000367630.9
VTA1	NM_001286371.2	c.697+7390A>G		intron_variant
VTA1	NM_001286372.2	c.523+7390A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VTA1	ENST00000367630.9	c.778+1940A>G		intron_variant		1	NM_016485.5	P1
VTA1	ENST00000367621.1	c.604+1940A>G		intron_variant		5
VTA1	ENST00000452973.6	c.523+7390A>G		intron_variant		2
VTA1	ENST00000620996.4	c.697+7390A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126650 AN: 152056 Hom.: 53384 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.833 AC: 126778 AN: 152172 Hom.: 53455 Cov.: 32 AF XY: 0.835 AC XY: 62131 AN XY: 74404

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.809

Alfa AF: 0.803 Hom.: 6323

Bravo AF: 0.839

Asia WGS AF: 0.842 AC: 2921 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.59

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: rs225694; hg19: chr6-142527142;