rs12518099

Variant names:

• chr5-90250292-A-G
• rs12518099
• ENST00000505712.5:n.136+10254T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-90250292-A-G
• chr5-90250292-A-T

Variant summary

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

The ENST00000505712.5(LINC01339):​n.136+10254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 150,384 control chromosomes in the GnomAD database, including 4,728 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 0.25 (4728 hom., cov: 30)
• Consequence: LINC01339 ENST00000505712.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

Genes affected

LINC01339 (HGNC:50549): (long intergenic non-protein coding RNA 1339)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01339	NR_120601.1	n.269+10254T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01339	ENST00000505712.5	n.136+10254T>C		intron_variant	Intron 3 of 5	2
LINC01339	ENST00000518436.5	n.179+10254T>C		intron_variant	Intron 3 of 4	3
LINC01339	ENST00000519336.1	n.270-5537T>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37310 AN: 150272 Hom.: 4721 Cov.: 30

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.248 AC: 37349 AN: 150384 Hom.: 4728 Cov.: 30 AF XY: 0.254 AC XY: 18625 AN XY: 73288

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.267

Alfa AF: 0.249 Hom.: 10811

Bravo AF: 0.250

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12518099; hg19: chr5-89546109;