rs1033391

Variant names:

• chr6-113438861-C-T
• rs1033391
• ENST00000421737.2:n.35+2560G>A

Variant summary

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

The ENST00000421737.2(LINC02518):​n.35+2560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,876 control chromosomes in the GnomAD database, including 11,632 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 0.38 (11632 hom., cov: 31)
• Consequence: LINC02518 ENST00000421737.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 6 publications found

Genes affected

LINC02518 (HGNC:53509): (long intergenic non-protein coding RNA 2518)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421737.2. 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
	LINC02518	ENST00000421737.2	TSL:3	n.35+2560G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58227 AN: 151758 Hom.: 11621 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.384 AC: 58274 AN: 151876 Hom.: 11632 Cov.: 31 AF XY: 0.378 AC XY: 28084 AN XY: 74226

African (AFR) AF: 0.288 AC: 11931 AN: 41436

American (AMR) AF: 0.417 AC: 6354 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2157 AN: 5148

South Asian (SAS) AF: 0.332 AC: 1603 AN: 4822

European-Finnish (FIN) AF: 0.323 AC: 3403 AN: 10540

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29738 AN: 67912

Other (OTH) AF: 0.455 AC: 957 AN: 2102

Alfa AF: 0.436 Hom.: 16933

Bravo AF: 0.389

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.40
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1033391; hg19: chr6-113760063; COSMIC: COSV60268620;