rs886424

chr6-30814225-C-T

Variant summary

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

The NR_130726.1(LINC00243):n.693G>A 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 0.0828 in 456,016 control chromosomes in the GnomAD database, including 2,309 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 0.085 (707 hom., cov: 32)
  • Exomes 𝑓: 0.082 (1602 hom.)
• Consequence: LINC00243 NR_130726.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00243	NR_130726.1	n.693G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-15453G>A		intron_variant, non_coding_transcript_variant		3
LINC00243	ENST00000399196.1	n.693G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12912 AN: 152130 Hom.: 707 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0735

GnomAD3 exomes AF: 0.0708 AC: 9693 AN: 136982 Hom.: 588 AF XY: 0.0712 AC XY: 5288 AN XY: 74310

Gnomad AFR exome AF: 0.0610

Gnomad AMR exome AF: 0.0303

Gnomad ASJ exome AF: 0.0619

Gnomad EAS exome AF: 0.000286

Gnomad SAS exome AF: 0.0208

Gnomad FIN exome AF: 0.0721

Gnomad NFE exome AF: 0.125

Gnomad OTH exome AF: 0.0794

GnomAD4 exome AF: 0.0818 AC: 24840 AN: 303768 Hom.: 1602 Cov.: 0 AF XY: 0.0763 AC XY: 13209 AN XY: 173024

Gnomad4 AFR exome AF: 0.0599

Gnomad4 AMR exome AF: 0.0303

Gnomad4 ASJ exome AF: 0.0652

Gnomad4 EAS exome AF: 0.000434

Gnomad4 SAS exome AF: 0.0200

Gnomad4 FIN exome AF: 0.0814

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.0877

GnomAD4 genome AF: 0.0848 AC: 12905 AN: 152248 Hom.: 707 Cov.: 32 AF XY: 0.0783 AC XY: 5827 AN XY: 74444

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.0414

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.110 Hom.: 2101

Bravo AF: 0.0826

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.76
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886424; hg19: chr6-30782002;