rs1152490

Variant names:

• chr14-56329516-C-A
• rs1152490
• ENST00000560924.2:n.473-906C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-56329516-C-A
• chr14-56329516-C-G
• chr14-56329516-C-T

Variant summary

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

The ENST00000560924.2(LINC02284):​n.473-906C>A variant causes a intron 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 ENST00000560924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560924.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02284	NR_187174.1		n.458-906C>A		intron	N/A
	LINC02284	NR_187175.1		n.420-906C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02284	ENST00000560924.2	TSL:4	n.473-906C>A		intron	N/A
	LINC02284	ENST00000663878.1		n.1075-906C>A		intron	N/A
	LINC02284	ENST00000664388.1		n.503-906C>A		intron	N/A

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

African (AFR) AF: 0.762 AC: 31598 AN: 41480

American (AMR) AF: 0.730 AC: 11155 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2722 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3850 AN: 5154

South Asian (SAS) AF: 0.823 AC: 3963 AN: 4818

European-Finnish (FIN) AF: 0.703 AC: 7437 AN: 10576

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52346 AN: 67976

Other (OTH) AF: 0.761 AC: 1605 AN: 2110

Alfa AF: 0.764 Hom.: 21347

Bravo AF: 0.758

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.57
PhyloP100		0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1152490;

hg19: chr14-56796234;