rs4836133

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-124996410-C-A
• chr5-124996410-C-G
• chr5-124996410-C-T

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>A variant causes a intron change. The variant allele was found at a frequency of 0.565 in 151,792 control chromosomes in the GnomAD database, including 26,018 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 0.56 (26018 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=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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>A		intron	N/A
	LINC02240	ENST00000825653.1		n.238-6492C>A		intron	N/A
	LINC02240	ENST00000825665.1		n.108-6492C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85580 AN: 151674 Hom.: 25957 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.565 AC: 85705 AN: 151792 Hom.: 26018 Cov.: 30 AF XY: 0.567 AC XY: 42045 AN XY: 74144

African (AFR) AF: 0.798 AC: 33023 AN: 41402

American (AMR) AF: 0.612 AC: 9321 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3462

East Asian (EAS) AF: 0.493 AC: 2543 AN: 5160

South Asian (SAS) AF: 0.501 AC: 2408 AN: 4802

European-Finnish (FIN) AF: 0.517 AC: 5417 AN: 10474

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29899 AN: 67940

Other (OTH) AF: 0.555 AC: 1168 AN: 2104

Alfa AF: 0.0943 Hom.: 2421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs4836133; hg19: chr5-124332103;