21-44934140-A-G

Variant summary

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

The NR_027128.1(LINC01547):n.977T>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 0.882 in 440,634 control chromosomes in the GnomAD database, including 171,802 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 0.90 (61324 hom., cov: 33)
  • Exomes 𝑓: 0.87 (110478 hom.)
• Consequence: LINC01547 NR_027128.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01547	NR_027128.1	n.977T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01547	ENST00000615847.3	n.1986T>C		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136393 AN: 152158 Hom.: 61263 Cov.: 33

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.872

GnomAD4 exome AF: 0.875 AC: 252243 AN: 288358 Hom.: 110478 Cov.: 0 AF XY: 0.874 AC XY: 141035 AN XY: 161310

Gnomad4 AFR exome AF: 0.968

Gnomad4 AMR exome AF: 0.923

Gnomad4 ASJ exome AF: 0.838

Gnomad4 EAS exome AF: 0.883

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.891

Gnomad4 NFE exome AF: 0.858

Gnomad4 OTH exome AF: 0.864

GnomAD4 genome AF: 0.896 AC: 136509 AN: 152276 Hom.: 61324 Cov.: 33 AF XY: 0.899 AC XY: 66916 AN XY: 74440

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.871

Alfa AF: 0.893 Hom.: 8610

Bravo AF: 0.900

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.96
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9974172; hg19: chr21-46354055;