Genetic Variant LINC01547:n.493T>C (chr21-44935795-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000330551.3(LINC01547):n.493T>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 0.388 in 469,170 control chromosomes in the GnomAD database, including 42,133 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 ( 21714 hom., cov: 32)

Exomes 𝑓: 0.34 ( 20419 hom. )

Consequence

LINC01547
ENST00000330551.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.562

Publications

11 publications found

Variant links:

COSMIC-nc: COSV52419630

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01547	NR_027128.1 link	n.417T>C		non_coding_transcript_exon_variant	Exon 2 of 4
LINC01547	NR_027129.1 link	n.561T>C		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01547	ENST00000330551.3 link	n.493T>C	non_coding_transcript_exon_variant	Exon 3 of 4	1
LINC01547	ENST00000615847.3 link	n.1426T>C	non_coding_transcript_exon_variant	Exon 2 of 4	1
LINC01547	ENST00000397841.5 link	n.417T>C	non_coding_transcript_exon_variant	Exon 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73669

AN:

151930

Hom.:

21668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.352

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.433

GnomAD2 exomes

AF:

0.362

AC:

56203

AN:

155364

AF XY:

0.343

show subpopulations

Gnomad AFR exome

AF:

0.841

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.358

Gnomad EAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.345

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.341

AC:

108048

AN:

317122

Hom.:

20419

Cov.:

AF XY:

0.324

AC XY:

58051

AN XY:

179182

show subpopulations

African (AFR)

AF:

0.828

AC:

6927

AN:

8364

American (AMR)

AF:

0.426

AC:

11440

AN:

26880

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

3868

AN:

10726

East Asian (EAS)

AF:

0.281

AC:

2541

AN:

9042

South Asian (SAS)

AF:

0.222

AC:

13182

AN:

59496

European-Finnish (FIN)

AF:

0.353

AC:

9876

AN:

28004

Middle Eastern (MID)

AF:

0.320

AC:

886

AN:

2766

European-Non Finnish (NFE)

AF:

0.344

AC:

54263

AN:

157644

Other (OTH)

AF:

0.357

AC:

5065

AN:

14200

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

2829

5657

8486

11314

14143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

362

724

1086

1448

1810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.485

AC:

73773

AN:

152048

Hom.:

21714

Cov.:

AF XY:

0.479

AC XY:

35628

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.837

AC:

34731

AN:

41508

American (AMR)

AF:

0.446

AC:

6803

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

1289

AN:

3470

East Asian (EAS)

AF:

0.268

AC:

1382

AN:

5162

South Asian (SAS)

AF:

0.209

AC:

1007

AN:

4824

European-Finnish (FIN)

AF:

0.352

AC:

3715

AN:

10566

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23490

AN:

67942

Other (OTH)

AF:

0.430

AC:

904

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1613

3226

4839

6452

8065

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.390

Hom.:

6917

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

-0.96

CADD

Benign

0.62

(source)

DANN

Benign

0.35

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over