6-142206005-A-G

Variant names:

• chr6-142206005-A-G
• rs225694
• NM_016485.5:c.778+1940A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016485.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VTA1	NM_016485.5	MANE Select	c.778+1940A>G		intron	N/A	NP_057569.2
	VTA1	NM_001286371.2		c.697+7390A>G		intron	N/A	NP_001273300.1	A0A087WY55
	VTA1	NM_001286372.2		c.523+7390A>G		intron	N/A	NP_001273301.1	Q9NP79-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VTA1	ENST00000367630.9	TSL:1 MANE Select	c.778+1940A>G		intron	N/A	ENSP00000356602.3	Q9NP79-1
	VTA1	ENST00000934453.1		c.772+1940A>G		intron	N/A	ENSP00000604512.1
	VTA1	ENST00000890565.1		c.778+1940A>G		intron	N/A	ENSP00000560624.1

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

African (AFR) AF: 0.947 AC: 39361 AN: 41548

American (AMR) AF: 0.834 AC: 12756 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2859 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5027 AN: 5180

South Asian (SAS) AF: 0.725 AC: 3489 AN: 4812

European-Finnish (FIN) AF: 0.859 AC: 9094 AN: 10588

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.760 AC: 51677 AN: 67964

Other (OTH) AF: 0.809 AC: 1711 AN: 2114

Alfa AF: 0.849 Hom.: 20458

Bravo AF: 0.839

Asia WGS AF: 0.842 AC: 2921 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs225694; hg19: chr6-142527142;