Genetic Variant LINC01755:n.240+32099C>T (chr1-55647101-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 ENST00000422374.1(LINC01755):n.240+32099C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,160 control chromosomes in the GnomAD database, including 24,826 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 0.56 ( 24826 hom., cov: 33)

Consequence

LINC01755
ENST00000422374.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

9 publications found

Variant links:

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

LINC01755 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01755	ENST00000422374.1 link	n.240+32099C>T	intron_variant	Intron 2 of 2	2
LINC01755	ENST00000634769.2 link	n.217-26159C>T	intron_variant	Intron 2 of 3	5
LINC01755	ENST00000643167.1 link	n.221-26159C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85123

AN:

152042

Hom.:

24817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.562

Gnomad EAS

AF:

0.826

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.564

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.560

AC:

85183

AN:

152160

Hom.:

24826

Cov.:

AF XY:

0.561

AC XY:

41754

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.421

AC:

17490

AN:

41504

American (AMR)

AF:

0.686

AC:

10491

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

1952

AN:

3472

East Asian (EAS)

AF:

0.825

AC:

4276

AN:

5182

South Asian (SAS)

AF:

0.463

AC:

2229

AN:

4818

European-Finnish (FIN)

AF:

0.604

AC:

6398

AN:

10584

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.596

AC:

40518

AN:

67986

Other (OTH)

AF:

0.560

AC:

1183

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1893

3787

5680

7574

9467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<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:

0.582

Hom.:

44126

Bravo

AF:

0.564

Asia WGS

AF:

0.586

AC:

2037

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.16

(source)

DANN

Benign

0.72

PhyloP100

-1.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over