5-24063344-G-A

Position:

• chr5-24063344-G-A

Variant summary

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

The NR_131245.1(LINC02899):​n.1557+82503G>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 0.678 in 151,940 control chromosomes in the GnomAD database, including 35,208 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 0.68 (35208 hom., cov: 32)
• Consequence: LINC02899 NR_131245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02899	NR_131245.1	n.1557+82503G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02899	ENST00000512559.5	n.1557+82503G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102943 AN: 151822 Hom.: 35162 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.678 AC: 103041 AN: 151940 Hom.: 35208 Cov.: 32 AF XY: 0.676 AC XY: 50237 AN XY: 74270

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.691

Alfa AF: 0.688 Hom.: 4487

Bravo AF: 0.672

Asia WGS AF: 0.634 AC: 2204 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7737173; hg19: chr5-24063453;