rs12526133

Positions:

• chr6-14281792-C-T

Variant summary

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

The NR_108097.1(LINC01108):​n.1796G>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 0.423 in 152,042 control chromosomes in the GnomAD database, including 16,444 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 0.42 (16444 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC01108 NR_108097.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

LINC01108 (HGNC:49234): (long intergenic non-protein coding RNA 1108)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01108	NR_108097.1	n.1796G>A		non_coding_transcript_exon_variant	2/2
LINC01108	NR_108096.1	n.2032G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01108	ENST00000427276.1	n.1487G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64291 AN: 151918 Hom.: 16438 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.472

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.423 AC: 64329 AN: 152036 Hom.: 16444 Cov.: 32 AF XY: 0.423 AC XY: 31470 AN XY: 74312

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.470

Alfa AF: 0.479 Hom.: 4227

Bravo AF: 0.410

Asia WGS AF: 0.267 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12526133; hg19: chr6-14282023;