rs12507634

Variant names:

• chr4-174150451-A-G
• rs12507634
• ENST00000511346.2:n.132+4136T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000515444.5(LINC02268):​n.86-30365T>C variant causes a intron 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 ENST00000515444.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515444.5. 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
	LINC02268	NR_125896.1		n.86-30365T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02268	ENST00000511346.2	TSL:3	n.132+4136T>C		intron	N/A
	LINC02268	ENST00000515444.5	TSL:2	n.86-30365T>C		intron	N/A
	LINC02268	ENST00000729418.1		n.129-30365T>C		intron	N/A

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

African (AFR) AF: 0.179 AC: 7441 AN: 41460

American (AMR) AF: 0.420 AC: 6400 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3466

East Asian (EAS) AF: 0.167 AC: 858 AN: 5136

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4828

European-Finnish (FIN) AF: 0.336 AC: 3543 AN: 10560

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27496 AN: 67844

Other (OTH) AF: 0.356 AC: 749 AN: 2104

Alfa AF: 0.329 Hom.: 5827

Bravo AF: 0.330

Asia WGS AF: 0.233 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.35
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12507634; hg19: chr4-175071602;