Variant rs9974152 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000615847.3(LINC01547):n.2056T>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 0.398 in 362,152 control chromosomes in the GnomAD database, including 34,850 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 ( 21723 hom., cov: 33)

Exomes 𝑓: 0.34 ( 13127 hom. )

Consequence

LINC01547
ENST00000615847.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Variant links:

Genes affected

LINC01547 (HGNC:):

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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.1047T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC01547	ENST00000615847.3 linkuse as main transcript	n.2056T>C	non_coding_transcript_exon_variant	4/4	1
LINC01547	ENST00000397841.5 linkuse as main transcript	n.1047T>C	non_coding_transcript_exon_variant	4/4	2
LINC01547	ENST00000654166.2 linkuse as main transcript	n.2224T>C	non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73704

AN:

151972

Hom.:

21677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.434

GnomAD4 exome

AF:

0.335

AC:

70404

AN:

210062

Hom.:

13127

Cov.:

AF XY:

0.320

AC XY:

36989

AN XY:

115620

show subpopulations

Gnomad4 AFR exome

AF:

0.835

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.353

Gnomad4 EAS exome

AF:

0.282

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.354

Gnomad4 NFE exome

AF:

0.344

Gnomad4 OTH exome

AF:

0.347

GnomAD4 genome

AF:

0.485

AC:

73808

AN:

152090

Hom.:

21723

Cov.:

AF XY:

0.480

AC XY:

35644

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.837

Gnomad4 AMR

AF:

0.448

Gnomad4 ASJ

AF:

0.370

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.351

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.300

Hom.:

1112

Bravo

AF:

0.513

Asia WGS

AF:

0.283

AC:

989

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

DANN

Benign

0.36

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