Genetic Variant ENST00000330551.3: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

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