rs1152490

chr14-56329516-C-Achr14-56329516-C-Gchr14-56329516-C-T

Variant summary

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

The ENST00000664388.1(LINC02284):n.503-906C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,078 control chromosomes in the GnomAD database, including 43,909 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 0.76 (43909 hom., cov: 32)
• Consequence: LINC02284 ENST00000664388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02284	XR_007064188.1	n.3120-906C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02284	ENST00000664388.1	n.503-906C>A		intron_variant, non_coding_transcript_variant
LINC02284	ENST00000560924.2	n.473-906C>A		intron_variant, non_coding_transcript_variant		4
LINC02284	ENST00000663878.1	n.1075-906C>A		intron_variant, non_coding_transcript_variant
LINC02284	ENST00000664536.1	n.920-906C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115322 AN: 151960 Hom.: 43863 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.759 AC: 115422 AN: 152078 Hom.: 43909 Cov.: 32 AF XY: 0.757 AC XY: 56320 AN XY: 74350

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.761

Alfa AF: 0.763 Hom.: 18848

Bravo AF: 0.758

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.8
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1152490; hg19: chr14-56796234;