rs2249017

chr12-40167418-A-G

Variant summary

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

The NR_146526.1(LINC02471):n.276A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,006 control chromosomes in the GnomAD database, including 30,338 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 0.62 (30338 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC02471 NR_146526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

Genes affected

LINC02471 (HGNC:53410): (long intergenic non-protein coding RNA 2471)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02471	NR_146526.1	n.276A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02471	ENST00000641941.1	n.231+11075A>G		intron_variant, non_coding_transcript_variant
LINC02471	ENST00000417422.2	n.270A>G		non_coding_transcript_exon_variant	2/2	3
LINC02471	ENST00000663154.3	n.364A>G		non_coding_transcript_exon_variant	2/2
LINC02471	ENST00000669755.1	n.261A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94482 AN: 151888 Hom.: 30319 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.615

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.622 AC: 94542 AN: 152006 Hom.: 30338 Cov.: 32 AF XY: 0.618 AC XY: 45920 AN XY: 74292

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.614

Alfa AF: 0.630 Hom.: 5269

Bravo AF: 0.598

Asia WGS AF: 0.488 AC: 1690 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249017; hg19: chr12-40561220;