Genetic Variant ENST00000471921.2:n.260C>T (chr3-160026651-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000471921.2(LINC01100):n.260C>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 0.74 in 456,322 control chromosomes in the GnomAD database, including 127,159 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 0.72 ( 40224 hom., cov: 32)

Exomes 𝑓: 0.75 ( 86935 hom. )

Consequence

LINC01100
ENST00000471921.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

9 publications found

Variant links:

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.103).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01100	NR_104132.1 link	n.138C>T		non_coding_transcript_exon_variant	Exon 2 of 3
IL12A-AS1	NR_108088.1 link	n.518-1117G>A		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01100	ENST00000471921.2 link	n.260C>T	non_coding_transcript_exon_variant	Exon 4 of 5	5
LINC01100	ENST00000740653.1 link	n.222C>T	non_coding_transcript_exon_variant	Exon 3 of 4
IL12A-AS1	ENST00000497452.5 link	n.518-1117G>A	intron_variant	Intron 3 of 9	2

Frequencies

GnomAD3 genomes

AF:

0.719

AC:

109152

AN:

151806

Hom.:

40213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.937

Gnomad AMR

AF:

0.754

Gnomad ASJ

AF:

0.806

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.625

Gnomad FIN

AF:

0.800

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.748

GnomAD2 exomes

AF:

0.732

AC:

98490

AN:

134520

AF XY:

0.729

show subpopulations

Gnomad AFR exome

AF:

0.532

Gnomad AMR exome

AF:

0.728

Gnomad ASJ exome

AF:

0.816

Gnomad EAS exome

AF:

0.599

Gnomad FIN exome

AF:

0.811

Gnomad NFE exome

AF:

0.803

Gnomad OTH exome

AF:

0.767

GnomAD4 exome

AF:

0.750

AC:

228264

AN:

304398

Hom.:

86935

Cov.:

AF XY:

0.741

AC XY:

128387

AN XY:

173332

show subpopulations

African (AFR)

AF:

0.537

AC:

4634

AN:

8628

American (AMR)

AF:

0.728

AC:

19868

AN:

27282

Ashkenazi Jewish (ASJ)

AF:

0.816

AC:

8800

AN:

10790

East Asian (EAS)

AF:

0.603

AC:

5552

AN:

9210

South Asian (SAS)

AF:

0.636

AC:

37967

AN:

59740

European-Finnish (FIN)

AF:

0.815

AC:

10429

AN:

12792

Middle Eastern (MID)

AF:

0.660

AC:

1836

AN:

2782

European-Non Finnish (NFE)

AF:

0.808

AC:

128348

AN:

158940

Other (OTH)

AF:

0.761

AC:

10830

AN:

14234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

3917

7833

11750

15666

19583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.719

AC:

109192

AN:

151924

Hom.:

40224

Cov.:

AF XY:

0.719

AC XY:

53368

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.549

AC:

22741

AN:

41422

American (AMR)

AF:

0.754

AC:

11522

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.806

AC:

2798

AN:

3472

East Asian (EAS)

AF:

0.608

AC:

3131

AN:

5148

South Asian (SAS)

AF:

0.625

AC:

3004

AN:

4806

European-Finnish (FIN)

AF:

0.800

AC:

8440

AN:

10554

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.809

AC:

54939

AN:

67934

Other (OTH)

AF:

0.743

AC:

1565

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1490

2980

4469

5959

7449

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.746

Hom.:

8690

Bravo

AF:

0.709

Asia WGS

AF:

0.575

AC:

2006

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.2

(source)

DANN

Benign

0.88

PhyloP100

0.21

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