rs55768019

Variant names:

• chr4-174106365-A-G
• rs55768019
• ENST00000503140.2:n.575+7676T>C

Variant summary

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

The ENST00000503140.2(LINC02268):​n.575+7676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,052 control chromosomes in the GnomAD database, including 14,462 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 0.43 (14462 hom., cov: 32)
• Consequence: LINC02268 ENST00000503140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 7 publications found

Genes affected

LINC02268 (HGNC:53183): (long intergenic non-protein coding RNA 2268)

ENSG00000295367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02268	NR_125896.1	n.276-8536T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02268	ENST00000503140.2	n.575+7676T>C		intron_variant	Intron 3 of 6	4
LINC02268	ENST00000515444.5	n.276-8536T>C		intron_variant	Intron 2 of 4	2
LINC02268	ENST00000656529.1	n.79-13068T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66046 AN: 151932 Hom.: 14458 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.435 AC: 66076 AN: 152052 Hom.: 14462 Cov.: 32 AF XY: 0.435 AC XY: 32345 AN XY: 74292

African (AFR) AF: 0.420 AC: 17422 AN: 41474

American (AMR) AF: 0.433 AC: 6608 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2541 AN: 5164

South Asian (SAS) AF: 0.405 AC: 1951 AN: 4822

European-Finnish (FIN) AF: 0.456 AC: 4813 AN: 10566

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29824 AN: 67970

Other (OTH) AF: 0.445 AC: 941 AN: 2114

Alfa AF: 0.427 Hom.: 1794

Bravo AF: 0.434

Asia WGS AF: 0.424 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs55768019; hg19: chr4-175027516;