rs8010248

Positions:

• chr14-50103507-A-C

Variant summary

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

The XM_017021640.3(VCPKMT):​c.*3061T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,140 control chromosomes in the GnomAD database, including 2,406 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 0.15 (2406 hom., cov: 32)
• Consequence: VCPKMT XM_017021640.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

Genes affected

VCPKMT (HGNC:20352): (valosin containing protein lysine methyltransferase) Enables ATPase binding activity and protein-lysine N-methyltransferase activity. Involved in negative regulation of ATPase activity and peptidyl-lysine trimethylation. Located in cytosol. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

LINC01588 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VCPKMT	XM_017021640.3	c.*3061T>G		3_prime_UTR_variant	6/6		XP_016877129.1
LINC01599	NR_131171.1	n.47+1490T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01588	ENST00000603228.3	n.106+1490T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23012 AN: 152022 Hom.: 2407 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.151 AC: 23007 AN: 152140 Hom.: 2406 Cov.: 32 AF XY: 0.155 AC XY: 11546 AN XY: 74368

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.177

Alfa AF: 0.157 Hom.: 276

Bravo AF: 0.163

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8010248; hg19: chr14-50570225;