rs3936060

Variant names:

• chr5-125011395-C-G
• rs3936060
• ENST00000642715.1:n.519+8382C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-125011395-C-G
• chr5-125011395-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642715.1(LINC02240):​n.519+8382C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,112 control chromosomes in the GnomAD database, including 5,696 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 0.25 (5696 hom., cov: 32)
• Consequence: LINC02240 ENST00000642715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000642715.1	n.519+8382C>G		intron_variant	Intron 2 of 3
LINC02240	ENST00000647105.1	n.205-30762C>G		intron_variant	Intron 1 of 6
LINC02240	ENST00000671535.1	n.619+7634C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37821 AN: 151994 Hom.: 5680 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37889 AN: 152112 Hom.: 5696 Cov.: 32 AF XY: 0.247 AC XY: 18337 AN XY: 74388

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.240

Alfa AF: 0.112 Hom.: 175

Bravo AF: 0.255

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3936060; hg19: chr5-124347088;