rs12483718

chr21-44934034-C-Gchr21-44934034-C-T

Variant summary

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

The NR_027128.1(LINC01547):n.1083G>C 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 0.167 in 313,972 control chromosomes in the GnomAD database, including 4,681 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 0.16 (2132 hom., cov: 33)
  • Exomes 𝑓: 0.17 (2549 hom.)
• Consequence: LINC01547 NR_027128.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

LINC01547 (HGNC:15707): (long intergenic non-protein coding RNA 1547) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01547	NR_027128.1	n.1083G>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01547	ENST00000615847.3	n.2092G>C		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24849 AN: 152032 Hom.: 2132 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.170 AC: 27585 AN: 161822 Hom.: 2549 Cov.: 0 AF XY: 0.170 AC XY: 15099 AN XY: 89062

Gnomad4 AFR exome AF: 0.109

Gnomad4 AMR exome AF: 0.175

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.169

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.163 AC: 24867 AN: 152150 Hom.: 2132 Cov.: 33 AF XY: 0.165 AC XY: 12275 AN XY: 74378

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.165

Alfa AF: 0.0890 Hom.: 120

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12483718; hg19: chr21-46353949; COSMIC: COSV57936840;