6-142220122-C-T

Variant names:

• chr6-142220122-C-T
• rs225710
• NM_016485.5:c.*1479C>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.*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
• Publications: 13 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=-0.9).
• 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 rank	MANE	Protein	UniProt
VTA1	NM_016485.5	c.*1479C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000367630.9	NP_057569.2
VTA1	NM_001286371.2	c.*1479C>T		3_prime_UTR_variant	Exon 7 of 7		NP_001273300.1
VTA1	NM_001286372.2	c.*1479C>T		3_prime_UTR_variant	Exon 6 of 6		NP_001273301.1

Ensembl

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

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.322 AC: 13361 AN: 41430

American (AMR) AF: 0.334 AC: 5105 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3468

East Asian (EAS) AF: 0.145 AC: 752 AN: 5176

South Asian (SAS) AF: 0.438 AC: 2107 AN: 4814

European-Finnish (FIN) AF: 0.528 AC: 5567 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34717 AN: 67952

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.479 Hom.: 68953

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
PhyloP100		-0.24
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: rs225710; hg19: chr6-142541259;