rs11834614

Variant names:

• chr12-68517297-T-C
• rs11834614
• ENST00000818919.1:n.132+21507A>G

Variant summary

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

The ENST00000818919.1(LINC02384):​n.132+21507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,170 control chromosomes in the GnomAD database, including 1,884 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 0.16 (1884 hom., cov: 32)
• Consequence: LINC02384 ENST00000818919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

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 = 0.175 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818919.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02384	ENST00000818919.1		n.132+21507A>G		intron	N/A
	LINC02384	ENST00000818920.1		n.122+21507A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23765 AN: 152052 Hom.: 1882 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.156 AC: 23782 AN: 152170 Hom.: 1884 Cov.: 32 AF XY: 0.155 AC XY: 11512 AN XY: 74402

African (AFR) AF: 0.179 AC: 7417 AN: 41524

American (AMR) AF: 0.123 AC: 1879 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.116 AC: 602 AN: 5178

South Asian (SAS) AF: 0.126 AC: 608 AN: 4826

European-Finnish (FIN) AF: 0.153 AC: 1615 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10516 AN: 68000

Other (OTH) AF: 0.155 AC: 327 AN: 2108

Alfa AF: 0.151 Hom.: 928

Bravo AF: 0.155

Asia WGS AF: 0.124 AC: 433 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	4.9
DANN	Benign	0.83
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11834614; hg19: chr12-68911077;