ENST00000652140.1:n.364+111A>G

Variant names:

• chr14-29245658-A-G
• rs10142843
• ENST00000652140.1:n.364+111A>G

Variant summary

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

The ENST00000652140.1(LINC02327):​n.364+111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,990 control chromosomes in the GnomAD database, including 25,688 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 0.58 (25688 hom., cov: 32)
• Consequence: LINC02327 ENST00000652140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 0 publications found

Genes affected

LINC02327 (HGNC:53247): (long intergenic non-protein coding RNA 2327)

ENSG00000257522 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652140.1. 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
	LINC02327	ENST00000652140.1		n.364+111A>G		intron	N/A
	ENSG00000257522	ENST00000652247.1		n.840+6961T>C		intron	N/A
	ENSG00000257522	ENST00000716712.1		n.335+132635T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87757 AN: 151872 Hom.: 25657 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.578 AC: 87832 AN: 151990 Hom.: 25688 Cov.: 32 AF XY: 0.572 AC XY: 42476 AN XY: 74280

African (AFR) AF: 0.490 AC: 20339 AN: 41474

American (AMR) AF: 0.583 AC: 8906 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2284 AN: 3466

East Asian (EAS) AF: 0.499 AC: 2577 AN: 5160

South Asian (SAS) AF: 0.640 AC: 3083 AN: 4816

European-Finnish (FIN) AF: 0.529 AC: 5585 AN: 10554

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43054 AN: 67926

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.618 Hom.: 87583

Bravo AF: 0.579

Asia WGS AF: 0.583 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.68
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10142843; hg19: chr14-29714864;