6-142220122-C-T

Position:

• chr6-142220122-C-T

Variant summary

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

The NM_016485.5(VTA1):​c.*1479C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,974 control chromosomes in the GnomAD database, including 15,068 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 0.43 (15068 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: VTA1 NM_016485.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VTA1	NM_016485.5	c.*1479C>T		3_prime_UTR_variant	8/8	ENST00000367630.9	NP_057569.2
VTA1	NM_001286371.2	c.*1479C>T		3_prime_UTR_variant	7/7		NP_001273300.1
VTA1	NM_001286372.2	c.*1479C>T		3_prime_UTR_variant	6/6		NP_001273301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VTA1	ENST00000367630.9	c.*1479C>T		3_prime_UTR_variant	8/8	1	NM_016485.5	ENSP00000356602	P1
VTA1	ENST00000452973.6	c.*1479C>T		3_prime_UTR_variant	6/6	2		ENSP00000395767
VTA1	ENST00000620996.4	c.*1479C>T		3_prime_UTR_variant	7/7	3		ENSP00000481525

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65359 AN: 151856 Hom.: 15058 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.422

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.430 AC: 65388 AN: 151974 Hom.: 15068 Cov.: 32 AF XY: 0.427 AC XY: 31733 AN XY: 74292

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.421

Alfa AF: 0.488 Hom.: 32029

Bravo AF: 0.406

Asia WGS AF: 0.302 AC: 1056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.52

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: rs225710; hg19: chr6-142541259;