15-95509513-C-T

Variant names:

• chr15-95509513-C-T
• rs933769
• ENST00000840556.1:n.235+31529C>T

Variant summary

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

The ENST00000840556.1(LINC00924):​n.235+31529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,048 control chromosomes in the GnomAD database, including 53,456 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 0.84 (53456 hom., cov: 31)
• Consequence: LINC00924 ENST00000840556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 12 publications found

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

ENSG00000309492 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840556.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00924	ENST00000840556.1		n.235+31529C>T		intron	N/A
	LINC00924	ENST00000840562.1		n.338+7862C>T		intron	N/A
	LINC00924	ENST00000840570.1		n.191-13386C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126923 AN: 151930 Hom.: 53407 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.835 AC: 127020 AN: 152048 Hom.: 53456 Cov.: 31 AF XY: 0.832 AC XY: 61796 AN XY: 74308

African (AFR) AF: 0.922 AC: 38296 AN: 41514

American (AMR) AF: 0.801 AC: 12244 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2677 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3330 AN: 5114

South Asian (SAS) AF: 0.689 AC: 3308 AN: 4800

European-Finnish (FIN) AF: 0.823 AC: 8684 AN: 10556

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55881 AN: 67988

Other (OTH) AF: 0.812 AC: 1719 AN: 2116

Alfa AF: 0.819 Hom.: 165585

Bravo AF: 0.837

Asia WGS AF: 0.605 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.16
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs933769; hg19: chr15-96052742;