5-15237631-C-T

Variant names:

• chr5-15237631-C-T
• rs10513204
• ENST00000511443.1:n.247+6018G>A

Variant summary

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

The ENST00000511443.1(LINC02149):​n.247+6018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,962 control chromosomes in the GnomAD database, including 10,117 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 0.36 (10117 hom., cov: 32)
• Consequence: LINC02149 ENST00000511443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 4 publications found

Genes affected

LINC02149 (HGNC:53010): (long intergenic non-protein coding RNA 2149)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511443.1. 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
	LINC02149	NR_109944.1		n.266+6018G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02149	ENST00000511443.1	TSL:1	n.247+6018G>A		intron	N/A
	LINC02149	ENST00000788346.1		n.405+5997G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54410 AN: 151844 Hom.: 10117 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.358 AC: 54426 AN: 151962 Hom.: 10117 Cov.: 32 AF XY: 0.351 AC XY: 26085 AN XY: 74272

African (AFR) AF: 0.275 AC: 11401 AN: 41448

American (AMR) AF: 0.329 AC: 5028 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3472

East Asian (EAS) AF: 0.173 AC: 892 AN: 5156

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4057 AN: 10550

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28964 AN: 67942

Other (OTH) AF: 0.393 AC: 828 AN: 2108

Alfa AF: 0.374 Hom.: 1883

Bravo AF: 0.349

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.75
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs10513204; hg19: chr5-15237740;