ENST00000512559.5:n.1557+41232T>C

Variant names:

• chr5-24022073-T-C
• rs1501947
• ENST00000512559.5:n.1557+41232T>C

Variant summary

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

The ENST00000512559.5(LINC02899):​n.1557+41232T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,904 control chromosomes in the GnomAD database, including 38,816 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 0.71 (38816 hom., cov: 32)
• Consequence: LINC02899 ENST00000512559.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02899	NR_131245.1	n.1557+41232T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02899	ENST00000512559.5	n.1557+41232T>C		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108033 AN: 151786 Hom.: 38755 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.712 AC: 108152 AN: 151904 Hom.: 38816 Cov.: 32 AF XY: 0.707 AC XY: 52510 AN XY: 74226

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.719

Alfa AF: 0.655 Hom.: 4012

Bravo AF: 0.711

Asia WGS AF: 0.643 AC: 2230 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
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: rs1501947; hg19: chr5-24022182;