6-142155699-A-T

Variant names:

• chr6-142155699-A-T
• rs4896580
• NM_016485.5:c.112+8300A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016485.5(VTA1):​c.112+8300A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,996 control chromosomes in the GnomAD database, including 5,840 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 0.26 (5840 hom., cov: 32)
• Consequence: VTA1 NM_016485.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTA1	NM_016485.5	c.112+8300A>T		intron_variant	Intron 1 of 7	ENST00000367630.9	NP_057569.2
VTA1	NM_001286371.2	c.112+8300A>T		intron_variant	Intron 1 of 6		NP_001273300.1
VTA1	NM_001286372.2	c.33+8300A>T		intron_variant	Intron 1 of 5		NP_001273301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VTA1	ENST00000367630.9	c.112+8300A>T		intron_variant	Intron 1 of 7	1	NM_016485.5	ENSP00000356602.3
VTA1	ENST00000620996.4	c.112+8300A>T		intron_variant	Intron 1 of 6	3		ENSP00000481525.1
VTA1	ENST00000367621.1	c.33+8300A>T		intron_variant	Intron 1 of 6	5		ENSP00000356593.1
VTA1	ENST00000452973.6	c.33+8300A>T		intron_variant	Intron 1 of 5	2		ENSP00000395767.2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39615 AN: 151878 Hom.: 5839 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.261 AC: 39635 AN: 151996 Hom.: 5840 Cov.: 32 AF XY: 0.269 AC XY: 19964 AN XY: 74264

African (AFR) AF: 0.267 AC: 11085 AN: 41474

American (AMR) AF: 0.321 AC: 4900 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.679 AC: 3491 AN: 5142

South Asian (SAS) AF: 0.166 AC: 798 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3600 AN: 10558

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14443 AN: 67960

Other (OTH) AF: 0.254 AC: 535 AN: 2110

Alfa AF: 0.243 Hom.: 580

Bravo AF: 0.266

Asia WGS AF: 0.354 AC: 1226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.62
PhyloP100		0.098
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: rs4896580; hg19: chr6-142476836;