Genetic Variant ENST00000330551.3: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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