rs1366262

Positions:

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

Variant summary

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

The NR_131245.1(LINC02899):​n.1558-11576C>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 0.698 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 NR_131245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

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

(HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02899	NR_131245.1	n.1558-11576C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02899	ENST00000512559.5	n.1558-11576C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000652008.2	n.255-25486G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.718

Alfa AF: 0.713 Hom.: 4838

Bravo AF: 0.693

Asia WGS AF: 0.641 AC: 2232 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	0.79
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1366262; hg19: chr5-24166370;