Genetic Variant ENST00000471921.2:n.140C>T (chr3-160020666-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000471921.2(LINC01100):n.140C>T 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 0.0601 in 456,474 control chromosomes in the GnomAD database, including 3,518 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 0.11 ( 2626 hom., cov: 32)

Exomes 𝑓: 0.033 ( 892 hom. )

Consequence

LINC01100
ENST00000471921.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

2 publications found

Variant links:

COSMIC-nc: COSV71829494

Genes affected

LINC01100 (HGNC:49224): (long intergenic non-protein coding RNA 1100)

LINC01100 links:

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

IL12A-AS1 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 (REVEL=0.009).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01100	NR_104132.1 link	n.18C>T		non_coding_transcript_exon_variant	Exon 1 of 3
IL12A-AS1	NR_108088.1 link	n.582+4804G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01100	ENST00000471921.2 link	n.140C>T	non_coding_transcript_exon_variant	Exon 3 of 5	5
LINC01100	ENST00000740652.1 link	n.118C>T	non_coding_transcript_exon_variant	Exon 2 of 3
LINC01100	ENST00000740653.1 link	n.102C>T	non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17234

AN:

151942

Hom.:

2611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.0750

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.000943

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00825

Gnomad OTH

AF:

0.0866

GnomAD2 exomes

AF:

0.0554

AC:

7450

AN:

134594

AF XY:

0.0445

show subpopulations

Gnomad AFR exome

AF:

0.364

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.00386

Gnomad EAS exome

AF:

0.0811

Gnomad FIN exome

AF:

0.00390

Gnomad NFE exome

AF:

0.00850

Gnomad OTH exome

AF:

0.0382

GnomAD4 exome

AF:

0.0334

AC:

10160

AN:

304414

Hom.:

892

Cov.:

AF XY:

0.0274

AC XY:

4747

AN XY:

173340

show subpopulations

African (AFR)

AF:

0.357

AC:

3078

AN:

8628

American (AMR)

AF:

0.139

AC:

3790

AN:

27282

Ashkenazi Jewish (ASJ)

AF:

0.00315

AC:

AN:

10790

East Asian (EAS)

AF:

0.0901

AC:

830

AN:

9210

South Asian (SAS)

AF:

0.0106

AC:

632

AN:

59742

European-Finnish (FIN)

AF:

0.00211

AC:

AN:

12798

Middle Eastern (MID)

AF:

0.0244

AC:

AN:

2782

European-Non Finnish (NFE)

AF:

0.00751

AC:

1193

AN:

158944

Other (OTH)

AF:

0.0357

AC:

508

AN:

14238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

505

1010

1516

2021

2526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

106

212

318

424

530

<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:

0.114

AC:

17285

AN:

152060

Hom.:

2626

Cov.:

AF XY:

0.109

AC XY:

8130

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.349

AC:

14439

AN:

41364

American (AMR)

AF:

0.106

AC:

1615

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00548

AC:

AN:

3470

East Asian (EAS)

AF:

0.0753

AC:

390

AN:

5176

South Asian (SAS)

AF:

0.0110

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.000943

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00823

AC:

560

AN:

68008

Other (OTH)

AF:

0.0862

AC:

182

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

576

1152

1727

2303

2879

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0489

Hom.:

2408

Bravo

AF:

0.137

Asia WGS

AF:

0.0590

AC:

206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.88

(source)

DANN

Benign

0.35

PhyloP100

-0.29

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