rs9332472

chr4-174104199-T-Achr4-174104199-T-C

Variant summary

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

The NR_125896.1(LINC02268):n.276-6370A>T variant causes a intron, non coding transcript 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 NR_125896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02268	NR_125896.1	n.276-6370A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02268	ENST00000515444.5	n.276-6370A>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.442

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332472; hg19: chr4-175025350;