rs1366262

Variant names:

• chr5-24166261-C-A
• rs1366262
• ENST00000512559.6:n.1558-11576C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-24166261-C-A
• chr5-24166261-C-G

Variant summary

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

The ENST00000512559.6(LINC02899):​n.1558-11576C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,850 control chromosomes in the GnomAD database, including 37,382 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 0.70 (37382 hom., cov: 31)
• Consequence: LINC02899 ENST00000512559.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 0 publications found

Genes affected

LINC02899 (HGNC:26630): (long intergenic non-protein coding RNA 2899)

ENSG00000286134 (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 (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512559.6. 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
	LINC02899	NR_131245.1		n.1558-11576C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02899	ENST00000512559.6	TSL:2	n.1558-11576C>A		intron	N/A
	ENSG00000286134	ENST00000652008.2		n.255-25486G>T		intron	N/A
	LINC02899	ENST00000779573.1		n.641-11576C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105887 AN: 151732 Hom.: 37328 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.698 AC: 105997 AN: 151850 Hom.: 37382 Cov.: 31 AF XY: 0.696 AC XY: 51613 AN XY: 74200

African (AFR) AF: 0.670 AC: 27767 AN: 41414

American (AMR) AF: 0.633 AC: 9654 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3099 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2603 AN: 5132

South Asian (SAS) AF: 0.703 AC: 3386 AN: 4816

European-Finnish (FIN) AF: 0.694 AC: 7330 AN: 10566

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.733 AC: 49778 AN: 67906

Other (OTH) AF: 0.718 AC: 1511 AN: 2104

Alfa AF: 0.711 Hom.: 5008

Bravo AF: 0.693

Asia WGS AF: 0.641 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.58
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs1366262; hg19: chr5-24166370;