5-90122201-A-T

Variant names:

• chr5-90122201-A-T
• rs2973361
• ENST00000813478.1:n.189-12833T>A

Variant summary

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

The ENST00000813478.1(LINC01339):​n.189-12833T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,046 control chromosomes in the GnomAD database, including 18,904 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 0.49 (18904 hom., cov: 32)
• Consequence: LINC01339 ENST00000813478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01339	ENST00000813478.1	n.189-12833T>A		intron_variant	Intron 2 of 4
LINC01339	ENST00000813481.1	n.249-12833T>A		intron_variant	Intron 3 of 6
LINC01339	ENST00000813482.1	n.192-19967T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74839 AN: 151930 Hom.: 18884 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.493 AC: 74891 AN: 152046 Hom.: 18904 Cov.: 32 AF XY: 0.494 AC XY: 36748 AN XY: 74332

African (AFR) AF: 0.399 AC: 16526 AN: 41462

American (AMR) AF: 0.601 AC: 9173 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1557 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3044 AN: 5186

South Asian (SAS) AF: 0.481 AC: 2315 AN: 4812

European-Finnish (FIN) AF: 0.493 AC: 5207 AN: 10568

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35359 AN: 67966

Other (OTH) AF: 0.505 AC: 1065 AN: 2110

Alfa AF: 0.494 Hom.: 2349

Bravo AF: 0.496

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2973361; hg19: chr5-89418018;