15-95532324-A-G

Variant names:

• chr15-95532324-A-G
• rs1834212
• ENST00000840556.1:n.236-32037A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000840556.1(LINC00924):​n.236-32037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,562 control chromosomes in the GnomAD database, including 8,443 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 0.32 (8443 hom., cov: 30)
• Consequence: LINC00924 ENST00000840556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 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.236-32037A>G		intron	N/A
	LINC00924	ENST00000840562.1		n.338+30673A>G		intron	N/A
	LINC00924	ENST00000840567.1		n.145+119A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49050 AN: 151448 Hom.: 8442 Cov.: 30

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.324 AC: 49052 AN: 151562 Hom.: 8443 Cov.: 30 AF XY: 0.318 AC XY: 23521 AN XY: 74072

African (AFR) AF: 0.238 AC: 9815 AN: 41276

American (AMR) AF: 0.279 AC: 4251 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1229 AN: 3454

East Asian (EAS) AF: 0.114 AC: 583 AN: 5136

South Asian (SAS) AF: 0.369 AC: 1770 AN: 4800

European-Finnish (FIN) AF: 0.311 AC: 3255 AN: 10476

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27098 AN: 67874

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.365 Hom.: 19193

Bravo AF: 0.311

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	19
DANN	Benign	0.77
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1834212; hg19: chr15-96075553;