Variant 21-44934034-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Variant links:

Genes affected

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

LINC01547 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
LINC01547	NR_027128.1 linkuse as main transcript	n.1083G>C		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24849

AN:

152032

Hom.:

2132

Cov.:

show subpopulations

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.:

AF XY:

0.170

AC XY:

15099

AN XY:

89062

show subpopulations

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.:

AF XY:

0.165

AC XY:

12275

AN XY:

74378

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over