15-66654488-C-T

Variant names:

• chr15-66654488-C-T
• rs2439378
• ENST00000558797.1:n.60-9874C>T

Variant summary

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

The ENST00000558797.1(LINC01169):​n.60-9874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,098 control chromosomes in the GnomAD database, including 25,506 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 0.58 (25506 hom., cov: 32)
• Consequence: LINC01169 ENST00000558797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 8 publications found

Genes affected

LINC01169 (HGNC:49541): (long intergenic non-protein coding RNA 1169)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558797.1. 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
	LINC01169	NR_110372.1		n.60-9874C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01169	ENST00000558797.1	TSL:1	n.60-9874C>T		intron	N/A
	LINC01169	ENST00000839031.1		n.266+9491C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87604 AN: 151980 Hom.: 25469 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.577 AC: 87696 AN: 152098 Hom.: 25506 Cov.: 32 AF XY: 0.580 AC XY: 43131 AN XY: 74348

African (AFR) AF: 0.634 AC: 26309 AN: 41502

American (AMR) AF: 0.544 AC: 8308 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2035 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2194 AN: 5152

South Asian (SAS) AF: 0.657 AC: 3169 AN: 4820

European-Finnish (FIN) AF: 0.604 AC: 6388 AN: 10582

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37275 AN: 67974

Other (OTH) AF: 0.560 AC: 1181 AN: 2110

Alfa AF: 0.548 Hom.: 35385

Bravo AF: 0.568

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs2439378; hg19: chr15-66946826;