5-125233645-T-C

Variant names:

• chr5-125233645-T-C
• rs1439609
• ENST00000647105.1:n.288-91707T>C

Variant summary

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

The ENST00000647105.1(LINC02240):​n.288-91707T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 151,802 control chromosomes in the GnomAD database, including 42,143 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 0.74 (42143 hom., cov: 31)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 3 publications found

Genes affected

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

LOC101927421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647105.1. 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
	LOC101927421	NR_109882.1		n.377+64019T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02240	ENST00000647105.1		n.288-91707T>C		intron	N/A
	LINC02240	ENST00000825646.1		n.278+64019T>C		intron	N/A
	LINC02240	ENST00000825648.1		n.276+64019T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112580 AN: 151682 Hom.: 42104 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.742 AC: 112669 AN: 151802 Hom.: 42143 Cov.: 31 AF XY: 0.737 AC XY: 54664 AN XY: 74156

African (AFR) AF: 0.819 AC: 33918 AN: 41424

American (AMR) AF: 0.696 AC: 10625 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2707 AN: 5164

South Asian (SAS) AF: 0.639 AC: 3072 AN: 4806

European-Finnish (FIN) AF: 0.717 AC: 7514 AN: 10478

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49607 AN: 67888

Other (OTH) AF: 0.760 AC: 1604 AN: 2110

Alfa AF: 0.734 Hom.: 51253

Bravo AF: 0.743

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1439609; hg19: chr5-124569338;