chr5-124996410-C-G

Position:

• chr5-124996410-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647105.1(LINC02240):​n.205-45747C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.84

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02240	ENST00000647105.1	n.205-45747C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0566

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0252 Hom.: 1426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4836133; hg19: chr5-124332103;