rs12637032

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986058	XR_001740584.1	n.8094-2897A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000794129.1	n.539-2897A>G		intron_variant	Intron 6 of 6
LINC01266	ENST00000794142.1	n.511-2897A>G		intron_variant	Intron 5 of 5

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 v4.3

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;