3-867062-A-G

Variant names:

• chr3-867062-A-G
• rs12637032
• ENST00000794129.1:n.539-2897A>G

Variant summary

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

The ENST00000794129.1(LINC01266):​n.539-2897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,054 control chromosomes in the GnomAD database, including 10,449 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 0.37 (10449 hom., cov: 32)
• Consequence: LINC01266 ENST00000794129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 3 publications found

Genes affected

LINC01266 (HGNC:50309): (long intergenic non-protein coding RNA 1266)

LOC107986058 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794129.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01266	ENST00000794129.1		n.539-2897A>G		intron	N/A
	LINC01266	ENST00000794142.1		n.511-2897A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55790 AN: 151936 Hom.: 10454 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.367 AC: 55812 AN: 152054 Hom.: 10449 Cov.: 32 AF XY: 0.372 AC XY: 27618 AN XY: 74308

African (AFR) AF: 0.382 AC: 15826 AN: 41482

American (AMR) AF: 0.422 AC: 6444 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2851 AN: 5178

South Asian (SAS) AF: 0.463 AC: 2236 AN: 4834

European-Finnish (FIN) AF: 0.340 AC: 3584 AN: 10552

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22862 AN: 67960

Other (OTH) AF: 0.367 AC: 773 AN: 2108

Alfa AF: 0.339 Hom.: 1543

Bravo AF: 0.368

Asia WGS AF: 0.499 AC: 1732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.47
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12637032; hg19: chr3-908745;