chr5-125582353-T-A

Variant names:

• chr5-125582353-T-A
• rs9327362
• ENST00000564199.1:n.325-18863T>A

Variant summary

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

The ENST00000564199.1(LINC02240):​n.325-18863T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 152,204 control chromosomes in the GnomAD database, including 296 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 0.047 (296 hom., cov: 33)
• Consequence: LINC02240 ENST00000564199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 2 publications found

Genes affected

LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

ENSG00000248752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564199.1. 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
	LINC02240	NR_109887.1		n.325-18863T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02240	ENST00000564199.1	TSL:2	n.325-18863T>A		intron	N/A
	LINC02240	ENST00000647105.1		n.549-1194T>A		intron	N/A
	ENSG00000248752	ENST00000651847.1		n.1076+29650A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7116 AN: 152086 Hom.: 295 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.00831

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0469 AC: 7141 AN: 152204 Hom.: 296 Cov.: 33 AF XY: 0.0453 AC XY: 3368 AN XY: 74408

African (AFR) AF: 0.111 AC: 4600 AN: 41520

American (AMR) AF: 0.0496 AC: 758 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3468

East Asian (EAS) AF: 0.0466 AC: 242 AN: 5188

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4818

European-Finnish (FIN) AF: 0.00831 AC: 88 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0175 AC: 1189 AN: 68020

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0322 Hom.: 21

Bravo AF: 0.0529

Asia WGS AF: 0.0440 AC: 151 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.061
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: rs9327362; hg19: chr5-124918046;