Genetic Variant LINC01547:n.661+11T>C (chr21-44935616-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.661+11T>C variant causes a intron 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
ENST00000330551.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.18

Publications

7 publications found

Variant links:

COSMIC-nc: COSV52419679

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 = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01547	NR_027128.1 link	n.585+11T>C		intron_variant	Intron 2 of 3
LINC01547	NR_027129.1 link	n.729+11T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01547	ENST00000330551.3 link	n.661+11T>C	intron_variant	Intron 3 of 3	1
LINC01547	ENST00000615847.3 link	n.1594+11T>C	intron_variant	Intron 2 of 3	1
LINC01547	ENST00000397841.5 link	n.585+11T>C	intron_variant	Intron 2 of 3	2

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

GnomAD2 exomes

AF:

0.358

AC:

18423

AN:

51464

AF XY:

0.338

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 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

African (AFR)

AF:

0.787

AC:

1393

AN:

1770

American (AMR)

AF:

0.397

AC:

2600

AN:

6552

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

945

AN:

2816

East Asian (EAS)

AF:

0.234

AC:

802

AN:

3422

South Asian (SAS)

AF:

0.213

AC:

7993

AN:

37608

European-Finnish (FIN)

AF:

0.350

AC:

8360

AN:

23856

Middle Eastern (MID)

AF:

0.311

AC:

649

AN:

2088

European-Non Finnish (NFE)

AF:

0.327

AC:

25702

AN:

78598

Other (OTH)

AF:

0.328

AC:

2292

AN:

6982

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

1519

3038

4557

6076

7595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<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:

73843

AN:

152120

Hom.:

21741

Cov.:

AF XY:

0.480

AC XY:

35684

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.837

AC:

34773

AN:

41540

American (AMR)

AF:

0.447

AC:

6826

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

1288

AN:

3468

East Asian (EAS)

AF:

0.267

AC:

1380

AN:

5160

South Asian (SAS)

AF:

0.209

AC:

1009

AN:

4826

European-Finnish (FIN)

AF:

0.351

AC:

3723

AN:

10592

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23488

AN:

67950

Other (OTH)

AF:

0.430

AC:

904

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1636

3272

4909

6545

8181

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.431

Hom.:

6734

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

(source)

DANN

Benign

0.26

PhyloP100

-3.2

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