rs6485671

Variant names:

• chr11-46258264-G-A
• rs6485671
• ENST00000527239.2:n.299-1723C>T

Variant summary

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

The ENST00000527239.2(LINC02489):​n.299-1723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,196 control chromosomes in the GnomAD database, including 11,379 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 0.29 (11379 hom., cov: 32)
• Consequence: LINC02489 ENST00000527239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 5 publications found

Genes affected

LINC02489 (HGNC:53470): (long intergenic non-protein coding RNA 2489)

ENSG00000302244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02489	NR_183622.1	n.185-1723C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02489	ENST00000527239.2	n.299-1723C>T		intron_variant	Intron 1 of 1	3
LINC02489	ENST00000686099.3	n.436-1723C>T		intron_variant	Intron 2 of 2
LINC02489	ENST00000785059.1	n.80-1723C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44662 AN: 152078 Hom.: 11337 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.294 AC: 44755 AN: 152196 Hom.: 11379 Cov.: 32 AF XY: 0.286 AC XY: 21268 AN XY: 74424

African (AFR) AF: 0.698 AC: 28975 AN: 41508

American (AMR) AF: 0.151 AC: 2316 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3472

East Asian (EAS) AF: 0.105 AC: 547 AN: 5190

South Asian (SAS) AF: 0.121 AC: 584 AN: 4814

European-Finnish (FIN) AF: 0.112 AC: 1191 AN: 10606

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9972 AN: 67994

Other (OTH) AF: 0.241 AC: 508 AN: 2110

Alfa AF: 0.210 Hom.: 13614

Bravo AF: 0.314

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.054
DANN	Benign	0.19
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6485671; hg19: chr11-46279815;