rs12469535

Variant names:

• chr2-242101996-G-A
• rs12469535
• ENST00000416103.2:n.134+6969G>A

Variant summary

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

The ENST00000416103.2(LINC01881):​n.134+6969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,934 control chromosomes in the GnomAD database, including 5,393 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 0.23 (5393 hom., cov: 32)
• Consequence: LINC01881 ENST00000416103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 11 publications found

Genes affected

LINC01881 (HGNC:52700): (long intergenic non-protein coding RNA 1881)

ENSG00000291147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01881	NR_130699.1	n.310+6969G>A		intron_variant	Intron 2 of 7
LINC01881	NR_130700.1	n.310+6969G>A		intron_variant	Intron 2 of 5
LINC01881	NR_130701.1	n.310+6969G>A		intron_variant	Intron 2 of 7
LINC01881	NR_130702.1	n.310+6969G>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01881	ENST00000416103.2	n.134+6969G>A		intron_variant	Intron 1 of 4	6
ENSG00000291147	ENST00000431796.6	n.259+6969G>A		intron_variant	Intron 2 of 6	4
ENSG00000291147	ENST00000433444.2	n.284+6969G>A		intron_variant	Intron 2 of 9	3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35238 AN: 151816 Hom.: 5366 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.232 AC: 35309 AN: 151934 Hom.: 5393 Cov.: 32 AF XY: 0.239 AC XY: 17781 AN XY: 74258

African (AFR) AF: 0.383 AC: 15870 AN: 41422

American (AMR) AF: 0.344 AC: 5243 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2165 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1512 AN: 4794

European-Finnish (FIN) AF: 0.173 AC: 1823 AN: 10552

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7478 AN: 67964

Other (OTH) AF: 0.222 AC: 467 AN: 2102

Alfa AF: 0.154 Hom.: 4236

Bravo AF: 0.251

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.18
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs12469535; hg19: chr2-243044147;