rs12507634

Positions:

• chr4-174150451-A-G
• chr4-174150451-A-T

Variant summary

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

The NR_125896.1(LINC02268):​n.86-30365T>C 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 0.327 in 151,822 control chromosomes in the GnomAD database, including 9,074 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 0.33 (9074 hom., cov: 32)
• Consequence: LINC02268 NR_125896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

Genes affected

(HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02268	NR_125896.1	n.86-30365T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000511346.1	n.51+4136T>C		intron_variant, non_coding_transcript_variant		3
LINC02268	ENST00000515444.5	n.86-30365T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49654 AN: 151704 Hom.: 9059 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.327 AC: 49695 AN: 151822 Hom.: 9074 Cov.: 32 AF XY: 0.325 AC XY: 24120 AN XY: 74186

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.356

Alfa AF: 0.355 Hom.: 2278

Bravo AF: 0.330

Asia WGS AF: 0.233 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12507634; hg19: chr4-175071602;