5-90250292-A-G

Variant names:

• chr5-90250292-A-G
• rs12518099
• ENST00000505712.6:n.238+10254T>C

Variant summary

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

The ENST00000505712.6(LINC01339):​n.238+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 ENST00000505712.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 25 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505712.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01339	NR_120601.1		n.269+10254T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01339	ENST00000505712.6	TSL:2	n.238+10254T>C		intron	N/A
	LINC01339	ENST00000518436.5	TSL:3	n.179+10254T>C		intron	N/A
	LINC01339	ENST00000519336.1	TSL:3	n.270-5537T>C		intron	N/A

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

African (AFR) AF: 0.225 AC: 9202 AN: 40820

American (AMR) AF: 0.284 AC: 4251 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3464

East Asian (EAS) AF: 0.426 AC: 2185 AN: 5124

South Asian (SAS) AF: 0.319 AC: 1519 AN: 4760

European-Finnish (FIN) AF: 0.255 AC: 2587 AN: 10160

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15852 AN: 67774

Other (OTH) AF: 0.267 AC: 560 AN: 2100

Alfa AF: 0.246 Hom.: 21039

Bravo AF: 0.250

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.47
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12518099; hg19: chr5-89546109;