ENST00000824537.1:n.547T>C

Variant names:

• chr12-30200961-A-G
• rs1843321
• ENST00000824537.1:n.547T>C

Variant summary

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

The ENST00000824537.1(LINC02386):​n.547T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 153,274 control chromosomes in the GnomAD database, including 11,897 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 (11873 hom., cov: 33)
  • Exomes 𝑓: 0.17 (24 hom.)
• Consequence: LINC02386 ENST00000824537.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 1 publications found

Genes affected

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

ENSG00000257262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824537.1. 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
	LINC02386	ENST00000824537.1		n.547T>C		non_coding_transcript_exon	Exon 1 of 2
	LINC02386	ENST00000824538.1		n.154T>C		non_coding_transcript_exon	Exon 1 of 2
	LINC02386	ENST00000824524.1		n.170-1322T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48913 AN: 151958 Hom.: 11857 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.170 AC: 204 AN: 1198 Hom.: 24 Cov.: 0 AF XY: 0.185 AC XY: 122 AN XY: 658

African (AFR) AF: 0.700 AC: 14 AN: 20

American (AMR) AF: 0.167 AC: 6 AN: 36

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 3 AN: 28

East Asian (EAS) AF: 0.750 AC: 21 AN: 28

South Asian (SAS) AF: 0.206 AC: 14 AN: 68

European-Finnish (FIN) AF: 0.182 AC: 8 AN: 44

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.141 AC: 129 AN: 916

Other (OTH) AF: 0.154 AC: 8 AN: 52

GnomAD4 genome AF: 0.322 AC: 48969 AN: 152076 Hom.: 11873 Cov.: 33 AF XY: 0.325 AC XY: 24180 AN XY: 74350

African (AFR) AF: 0.659 AC: 27337 AN: 41484

American (AMR) AF: 0.205 AC: 3128 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3468

East Asian (EAS) AF: 0.638 AC: 3281 AN: 5146

South Asian (SAS) AF: 0.283 AC: 1364 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10584

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10111 AN: 67968

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.215 Hom.: 1084

Bravo AF: 0.334

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.40
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1843321; hg19: chr12-30353894;