4-96312526-T-C

Variant names:

• chr4-96312526-T-C
• rs2048022
• ENST00000513393.1:n.94+1732T>C

Variant summary

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

The ENST00000513393.1(LINC02267):​n.94+1732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,658 control chromosomes in the GnomAD database, including 13,312 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 0.41 (13312 hom., cov: 31)
• Consequence: LINC02267 ENST00000513393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 5 publications found

Genes affected

LINC02267 (HGNC:53181): (long intergenic non-protein coding RNA 2267)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513393.1. 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
	LINC02267	NR_147149.1		n.92+1732T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02267	ENST00000513393.1	TSL:3	n.94+1732T>C		intron	N/A
	LINC02267	ENST00000522173.1	TSL:3	n.63+1732T>C		intron	N/A
	LINC02267	ENST00000754345.1		n.301+1732T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61379 AN: 151540 Hom.: 13289 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.405 AC: 61441 AN: 151658 Hom.: 13312 Cov.: 31 AF XY: 0.408 AC XY: 30227 AN XY: 74092

African (AFR) AF: 0.524 AC: 21658 AN: 41304

American (AMR) AF: 0.461 AC: 7013 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3235 AN: 5150

South Asian (SAS) AF: 0.444 AC: 2127 AN: 4788

European-Finnish (FIN) AF: 0.348 AC: 3665 AN: 10542

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21314 AN: 67902

Other (OTH) AF: 0.418 AC: 877 AN: 2096

Alfa AF: 0.310 Hom.: 3794

Bravo AF: 0.419

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.75
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2048022; hg19: chr4-97233677;