15-88603303-C-A

Variant names:

• chr15-88603303-C-A
• rs11637762
• ENST00000506090.6:n.468+94G>T

Variant summary

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

The ENST00000506090.6(LINC01586):​n.468+94G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,882 control chromosomes in the GnomAD database, including 14,725 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 0.44 (14725 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01586 ENST00000506090.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 7 publications found

Genes affected

LINC01586 (HGNC:51434): (long intergenic non-protein coding RNA 1586)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506090.6. 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
	LINC01586	NR_120369.1		n.343+94G>T		intron	N/A
	LINC01586	NR_120370.1		n.333+94G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01586	ENST00000506090.6	TSL:2	n.468+94G>T		intron	N/A
	LINC01586	ENST00000560368.1	TSL:3	n.333+94G>T		intron	N/A
	LINC01586	ENST00000660022.1		n.119+94G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66631 AN: 151764 Hom.: 14724 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.439 AC: 66662 AN: 151882 Hom.: 14725 Cov.: 32 AF XY: 0.440 AC XY: 32659 AN XY: 74216

African (AFR) AF: 0.456 AC: 18875 AN: 41388

American (AMR) AF: 0.422 AC: 6432 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3719 AN: 5182

South Asian (SAS) AF: 0.409 AC: 1971 AN: 4822

European-Finnish (FIN) AF: 0.452 AC: 4752 AN: 10512

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27961 AN: 67958

Other (OTH) AF: 0.449 AC: 945 AN: 2104

Alfa AF: 0.353 Hom.: 1466

Bravo AF: 0.441

Asia WGS AF: 0.569 AC: 1976 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs11637762; hg19: chr15-89146534;