chr12-30220071-T-C

Variant names:

• chr12-30220071-T-C
• rs1157480
• ENST00000824524.1:n.170-20432A>G

Variant summary

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

The ENST00000824524.1(LINC02386):​n.170-20432A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,998 control chromosomes in the GnomAD database, including 45,183 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 0.77 (45183 hom., cov: 30)
• Consequence: LINC02386 ENST00000824524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 5 publications found

Genes affected

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824524.1. 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
	LINC02386	ENST00000824524.1		n.170-20432A>G		intron	N/A
	LINC02386	ENST00000824525.1		n.224-20432A>G		intron	N/A
	LINC02386	ENST00000824526.1		n.315+12705A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116230 AN: 151880 Hom.: 45112 Cov.: 30

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.766 AC: 116362 AN: 151998 Hom.: 45183 Cov.: 30 AF XY: 0.764 AC XY: 56743 AN XY: 74258

African (AFR) AF: 0.900 AC: 37355 AN: 41494

American (AMR) AF: 0.773 AC: 11779 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4293 AN: 5168

South Asian (SAS) AF: 0.735 AC: 3539 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7139 AN: 10524

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47259 AN: 67968

Other (OTH) AF: 0.758 AC: 1596 AN: 2106

Alfa AF: 0.709 Hom.: 81032

Bravo AF: 0.779

Asia WGS AF: 0.799 AC: 2773 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1157480; hg19: chr12-30373004;