rs12469535

Positions:

• chr2-242101996-G-A

Variant summary

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

The NR_130701.1(LINC01881):​n.310+6969G>A 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 0.232 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 NR_130701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01881	NR_130701.1	n.310+6969G>A		intron_variant, non_coding_transcript_variant
LINC01881	NR_130699.1	n.310+6969G>A		intron_variant, non_coding_transcript_variant
LINC01881	NR_130700.1	n.310+6969G>A		intron_variant, non_coding_transcript_variant
LINC01881	NR_130702.1	n.310+6969G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01881	ENST00000416103.2	n.134+6969G>A		intron_variant, non_coding_transcript_variant
	ENST00000692555.1	n.301+6969G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.222

Alfa AF: 0.143 Hom.: 2797

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12469535; hg19: chr2-243044147;