ENST00000664388.1:n.666-6220A>C

Variant names:

• chr14-56419968-A-C
• rs17832777
• ENST00000664388.1:n.666-6220A>C

Variant summary

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

The ENST00000664388.1(LINC02284):​n.666-6220A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,182 control chromosomes in the GnomAD database, including 2,495 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 0.18 (2495 hom., cov: 32)
• Consequence: LINC02284 ENST00000664388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

Genes affected

LINC02284 (HGNC:53201): (long intergenic non-protein coding RNA 2284)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02284	NR_187174.1	n.621-6220A>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02284	ENST00000664388.1	n.666-6220A>C		intron_variant	Intron 6 of 6
LINC02284	ENST00000732419.1	n.575-6220A>C		intron_variant	Intron 5 of 5
LINC02284	ENST00000732420.1	n.1126-6220A>C		intron_variant	Intron 8 of 8
LINC02284	ENST00000732421.1	n.677-3220A>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26765 AN: 152064 Hom.: 2497 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.176 AC: 26774 AN: 152182 Hom.: 2495 Cov.: 32 AF XY: 0.176 AC XY: 13126 AN XY: 74402

African (AFR) AF: 0.175 AC: 7261 AN: 41518

American (AMR) AF: 0.187 AC: 2854 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.0690 AC: 357 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1067 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1994 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11997 AN: 68008

Other (OTH) AF: 0.177 AC: 373 AN: 2110

Alfa AF: 0.174 Hom.: 5019

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.22
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17832777; hg19: chr14-56886686;