ENST00000503140.2:n.576-6370A>T

Variant names:

• chr4-174104199-T-A
• rs9332472
• ENST00000503140.2:n.576-6370A>T

Variant summary

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

The ENST00000503140.2(LINC02268):​n.576-6370A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,878 control chromosomes in the GnomAD database, including 14,354 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 (14354 hom., cov: 31)
• Consequence: LINC02268 ENST00000503140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 4 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=-0.82).
• 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.276-6370A>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02268	ENST00000503140.2	n.576-6370A>T		intron_variant	Intron 3 of 6	4
LINC02268	ENST00000515444.5	n.276-6370A>T		intron_variant	Intron 2 of 4	2
LINC02268	ENST00000656529.1	n.79-10902A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65728 AN: 151758 Hom.: 14350 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.433 AC: 65760 AN: 151878 Hom.: 14354 Cov.: 31 AF XY: 0.434 AC XY: 32237 AN XY: 74220

African (AFR) AF: 0.418 AC: 17304 AN: 41412

American (AMR) AF: 0.431 AC: 6572 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2536 AN: 5158

South Asian (SAS) AF: 0.406 AC: 1958 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4808 AN: 10520

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29734 AN: 67938

Other (OTH) AF: 0.442 AC: 932 AN: 2110

Alfa AF: 0.427 Hom.: 1723

Bravo AF: 0.432

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.86
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs9332472; hg19: chr4-175025350;