ENST00000769287.1:n.262T>G

Variant names:

• chr14-50103507-A-C
• rs8010248
• ENST00000769287.1:n.262T>G

Variant summary

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

The ENST00000769287.1(LINC01588):​n.262T>G variant causes a non coding transcript exon 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: LINC01588 ENST00000769287.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 0 publications found

Genes affected

LINC01588 (HGNC:27503): (long intergenic non-protein coding RNA 1588)

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]

LINC01599 (HGNC:27285): (long intergenic non-protein coding RNA 1599)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
VCPKMT	XM_017021640.3	c.*3061T>G		3_prime_UTR_variant	Exon 6 of 6		XP_016877129.1
LINC01599	NR_131171.1	n.47+1490T>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01588	ENST00000769287.1	n.262T>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01588	ENST00000769288.1	n.318T>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01588	ENST00000603228.3	n.106+1490T>G		intron_variant	Intron 1 of 8	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

African (AFR) AF: 0.0385 AC: 1600 AN: 41528

American (AMR) AF: 0.325 AC: 4959 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5174

South Asian (SAS) AF: 0.178 AC: 859 AN: 4816

European-Finnish (FIN) AF: 0.153 AC: 1616 AN: 10578

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11503 AN: 67994

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.152 Hom.: 277

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs8010248; hg19: chr14-50570225;