chr5-124996410-C-G

Variant names:

• chr5-124996410-C-G
• rs4836133
• ENST00000647105.1:n.205-45747C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647105.1(LINC02240):​n.205-45747C>G variant causes a intron change. The variant allele was found at a frequency of 0.0757 in 151,848 control chromosomes in the GnomAD database, including 538 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 0.076 (538 hom., cov: 30)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.84
• Publications: 98 publications found

Genes affected

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

ENSG00000288008 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02240	ENST00000647105.1		n.205-45747C>G		intron	N/A
	LINC02240	ENST00000825653.1		n.238-6492C>G		intron	N/A
	LINC02240	ENST00000825665.1		n.108-6492C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11488 AN: 151730 Hom.: 536 Cov.: 30

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0757 AC: 11490 AN: 151848 Hom.: 538 Cov.: 30 AF XY: 0.0759 AC XY: 5633 AN XY: 74172

African (AFR) AF: 0.0367 AC: 1521 AN: 41424

American (AMR) AF: 0.0776 AC: 1183 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5162

South Asian (SAS) AF: 0.117 AC: 562 AN: 4804

European-Finnish (FIN) AF: 0.0566 AC: 593 AN: 10476

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0853 AC: 5798 AN: 67964

Other (OTH) AF: 0.0855 AC: 180 AN: 2106

Alfa AF: 0.0198 Hom.: 2421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		3.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4836133;

hg19: chr5-124332103;