Genetic Variant ENST00000451980.5:n.109+82T>C (chr21-33170482-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 ENST00000451980.5(LINC01548):n.109+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 309,544 control chromosomes in the GnomAD database, including 7,308 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 0.22 ( 4078 hom., cov: 31)

Exomes 𝑓: 0.19 ( 3230 hom. )

Consequence

LINC01548
ENST00000451980.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

Publications

4 publications found

Variant links:

Genes affected

LINC01548 (HGNC:1296): (long intergenic non-protein coding RNA 1548)

LINC01548 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01548	NR_024102.1 link	n.-246T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01548	ENST00000451980.5 link	n.109+82T>C	intron_variant	Intron 1 of 4	5
LINC01548	ENST00000796078.1 link	n.92+82T>C	intron_variant	Intron 1 of 3
LINC01548	ENST00000796079.1 link	n.88+82T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33495

AN:

151784

Hom.:

4076

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.191

AC:

30180

AN:

157642

Hom.:

3230

AF XY:

0.189

AC XY:

16066

AN XY:

85204

show subpopulations

African (AFR)

AF:

0.286

AC:

1387

AN:

4844

American (AMR)

AF:

0.149

AC:

1567

AN:

10518

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

954

AN:

3610

East Asian (EAS)

AF:

0.00178

AC:

AN:

7856

South Asian (SAS)

AF:

0.166

AC:

4898

AN:

29482

European-Finnish (FIN)

AF:

0.152

AC:

949

AN:

6238

Middle Eastern (MID)

AF:

0.205

AC:

111

AN:

542

European-Non Finnish (NFE)

AF:

0.216

AC:

18747

AN:

86732

Other (OTH)

AF:

0.199

AC:

1553

AN:

7820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1126

2252

3379

4505

5631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

264

396

528

660

<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:

0.221

AC:

33520

AN:

151902

Hom.:

4078

Cov.:

AF XY:

0.215

AC XY:

15968

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.289

AC:

11959

AN:

41382

American (AMR)

AF:

0.184

AC:

2810

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

928

AN:

3472

East Asian (EAS)

AF:

0.00232

AC:

AN:

5182

South Asian (SAS)

AF:

0.157

AC:

753

AN:

4810

European-Finnish (FIN)

AF:

0.137

AC:

1443

AN:

10564

Middle Eastern (MID)

AF:

0.209

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.220

AC:

14949

AN:

67928

Other (OTH)

AF:

0.219

AC:

460

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1288

2577

3865

5154

6442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.221

Hom.:

7326

Bravo

AF:

0.226

Asia WGS

AF:

0.0860

AC:

298

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

(source)

DANN

Benign

0.64

PhyloP100

-0.17

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