Variant rs11088970 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.585+11T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 315,812 control chromosomes in the GnomAD database, including 30,400 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 0.49 ( 21741 hom., cov: 33)

Exomes 𝑓: 0.31 ( 8659 hom. )

Consequence

LINC01547
NR_027128.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.18

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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.585+11T>C		intron_variant, non_coding_transcript_variant
LINC01547	NR_027129.1 linkuse as main transcript	n.729+11T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000615847.3 linkuse as main transcript	n.1594+11T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73739

AN:

152002

Hom.:

21695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.434

GnomAD3 exomes

AF:

0.358

AC:

18423

AN:

51464

Hom.:

3952

AF XY:

0.338

AC XY:

8312

AN XY:

24618

show subpopulations

Gnomad AFR exome

AF:

0.833

Gnomad AMR exome

AF:

0.392

Gnomad ASJ exome

AF:

0.318

Gnomad EAS exome

AF:

0.231

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.312

GnomAD4 exome

AF:

0.310

AC:

50736

AN:

163692

Hom.:

8659

Cov.:

AF XY:

0.296

AC XY:

27075

AN XY:

91590

show subpopulations

Gnomad4 AFR exome

AF:

0.787

Gnomad4 AMR exome

AF:

0.397

Gnomad4 ASJ exome

AF:

0.336

Gnomad4 EAS exome

AF:

0.234

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.485

AC:

73843

AN:

152120

Hom.:

21741

Cov.:

AF XY:

0.480

AC XY:

35684

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.837

Gnomad4 AMR

AF:

0.447

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.351

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.424

Hom.:

5284

Bravo

AF:

0.513

Asia WGS

AF:

0.283

AC:

987

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.10

DANN

Benign

0.26

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