dbSNP rs9653442: LINC01104:n.567+85C>T (chr2-100208905-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 ENST00000452354.5(LINC01104):n.567+85C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,142 control chromosomes in the GnomAD database, including 17,297 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 0.46 ( 17295 hom., cov: 33)

Exomes 𝑓: 0.75 ( 2 hom. )

Consequence

LINC01104
ENST00000452354.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.593

Publications

77 publications found

Variant links:

Genes affected

LINC01104 (HGNC:49226): (long intergenic non-protein coding RNA 1104)

LINC01104 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01104	NR_103730.1 link	n.567+85C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01104	ENST00000452354.5 link	n.567+85C>T	intron_variant	Intron 1 of 2	1
LINC01104	ENST00000841887.1 link	n.669+85C>T	intron_variant	Intron 1 of 4
LINC01104	ENST00000841888.1 link	n.605+85C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.462

AC:

70268

AN:

152016

Hom.:

17290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.476

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.462

AC:

70302

AN:

152134

Hom.:

17295

Cov.:

AF XY:

0.463

AC XY:

34444

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.306

AC:

12692

AN:

41498

American (AMR)

AF:

0.414

AC:

6323

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

1930

AN:

3470

East Asian (EAS)

AF:

0.610

AC:

3154

AN:

5170

South Asian (SAS)

AF:

0.415

AC:

2003

AN:

4822

European-Finnish (FIN)

AF:

0.568

AC:

6019

AN:

10594

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.539

AC:

36617

AN:

67986

Other (OTH)

AF:

0.476

AC:

1004

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1896

3793

5689

7586

9482

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.514

Hom.:

62192

Bravo

AF:

0.445

Asia WGS

AF:

0.458

AC:

1593

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.81

(source)

DANN

Benign

0.46

PhyloP100

-0.59

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