rs6485671

Positions:

• chr11-46258264-G-A

Variant summary

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

The NR_183622.1(LINC02489):​n.185-1723C>T 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 0.294 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 NR_183622.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02489	NR_183622.1	n.185-1723C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02489	ENST00000527239.1	n.168-1723C>T		intron_variant, non_coding_transcript_variant		3
LINC02489	ENST00000686099.2	n.185-1723C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.241

Alfa AF: 0.169 Hom.: 4678

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6485671; hg19: chr11-46279815;