rs454217

Variant names:

• chr12-92324782-C-T
• rs454217
• ENST00000615716.2:n.386+32749G>A

Variant summary

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

The ENST00000847433.1(LINC02391):​n.452+32749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,032 control chromosomes in the GnomAD database, including 33,769 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 0.66 (33769 hom., cov: 31)
• Consequence: LINC02391 ENST00000847433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

LINC02391 (HGNC:53318): (long intergenic non-protein coding RNA 2391)

ENSG00000310158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847433.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02391	ENST00000615716.2	TSL:5	n.386+32749G>A		intron	N/A
	LINC02391	ENST00000847433.1		n.452+32749G>A		intron	N/A
	LINC02391	ENST00000847434.1		n.387-30280G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99748 AN: 151914 Hom.: 33725 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.657 AC: 99858 AN: 152032 Hom.: 33769 Cov.: 31 AF XY: 0.653 AC XY: 48508 AN XY: 74312

African (AFR) AF: 0.831 AC: 34461 AN: 41468

American (AMR) AF: 0.572 AC: 8738 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4069 AN: 5180

South Asian (SAS) AF: 0.557 AC: 2679 AN: 4812

European-Finnish (FIN) AF: 0.574 AC: 6053 AN: 10554

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39641 AN: 67962

Other (OTH) AF: 0.638 AC: 1348 AN: 2112

Alfa AF: 0.623 Hom.: 5094

Bravo AF: 0.666

Asia WGS AF: 0.695 AC: 2417 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	4.9
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs454217;

hg19: chr12-92718558;