rs1319036

Variant names:

• chr8-69239817-C-T
• rs1319036
• ENST00000836183.1:n.433+14381G>A

Variant summary

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

The ENST00000836183.1(LINC01592):​n.433+14381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,122 control chromosomes in the GnomAD database, including 35,531 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 0.67 (35531 hom., cov: 33)
• Consequence: LINC01592 ENST00000836183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 2 publications found

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 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
LINC01592	ENST00000836183.1	n.433+14381G>A		intron_variant	Intron 1 of 1
LINC01592	ENST00000836188.1	n.518+14381G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102149 AN: 152004 Hom.: 35522 Cov.: 33

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.672 AC: 102201 AN: 152122 Hom.: 35531 Cov.: 33 AF XY: 0.668 AC XY: 49693 AN XY: 74340

African (AFR) AF: 0.507 AC: 21040 AN: 41488

American (AMR) AF: 0.728 AC: 11130 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2609 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2169 AN: 5158

South Asian (SAS) AF: 0.621 AC: 2999 AN: 4830

European-Finnish (FIN) AF: 0.687 AC: 7276 AN: 10588

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52475 AN: 67990

Other (OTH) AF: 0.717 AC: 1512 AN: 2108

Alfa AF: 0.698 Hom.: 4907

Bravo AF: 0.670

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1319036; hg19: chr8-70152052;