15-95613139-A-G

Variant names:

• chr15-95613139-A-G
• rs4321143
• ENST00000840569.1:n.211-2368A>G

Variant summary

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

The ENST00000840569.1(LINC00924):​n.211-2368A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,116 control chromosomes in the GnomAD database, including 6,275 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 0.28 (6275 hom., cov: 33)
• Consequence: LINC00924 ENST00000840569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 10 publications found

Genes affected

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

ENSG00000309432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840569.1. 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	ENST00000840569.1		n.211-2368A>G		intron	N/A
	ENSG00000309432	ENST00000841104.1		n.327-18394T>C		intron	N/A
	ENSG00000309432	ENST00000841105.1		n.207-18394T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43009 AN: 151998 Hom.: 6265 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.283 AC: 43049 AN: 152116 Hom.: 6275 Cov.: 33 AF XY: 0.274 AC XY: 20382 AN XY: 74358

African (AFR) AF: 0.334 AC: 13835 AN: 41480

American (AMR) AF: 0.260 AC: 3975 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1212 AN: 5142

South Asian (SAS) AF: 0.203 AC: 977 AN: 4818

European-Finnish (FIN) AF: 0.165 AC: 1748 AN: 10600

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19200 AN: 67992

Other (OTH) AF: 0.282 AC: 596 AN: 2116

Alfa AF: 0.280 Hom.: 19047

Bravo AF: 0.293

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.51
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4321143; hg19: chr15-96156368;