dbSNP rs7662358: LINC01060:n.88-11016C>A (chr4-188669705-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503580.1(LINC01060):n.88-11016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,484 control chromosomes in the GnomAD database, including 2,069 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 0.16 ( 2069 hom., cov: 32)

Consequence

LINC01060
ENST00000503580.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.408

Publications

1 publications found

Variant links:

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

LINC01060 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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
LINC01060	ENST00000503580.1 link	n.88-11016C>A	intron_variant	Intron 1 of 1	3
LINC01060	ENST00000664177.2 link	n.338-10578C>A	intron_variant	Intron 3 of 3
LINC01060	ENST00000692519.2 link	n.389-10578C>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24569

AN:

151366

Hom.:

2064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0828

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.162

AC:

24599

AN:

151484

Hom.:

2069

Cov.:

AF XY:

0.158

AC XY:

11664

AN XY:

74000

show subpopulations

African (AFR)

AF:

0.186

AC:

7669

AN:

41252

American (AMR)

AF:

0.145

AC:

2207

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.0828

AC:

287

AN:

3466

East Asian (EAS)

AF:

0.107

AC:

547

AN:

5128

South Asian (SAS)

AF:

0.117

AC:

559

AN:

4796

European-Finnish (FIN)

AF:

0.139

AC:

1457

AN:

10458

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11371

AN:

67858

Other (OTH)

AF:

0.169

AC:

356

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1048

2096

3145

4193

5241

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.158

Hom.:

3037

Bravo

AF:

0.161

Asia WGS

AF:

0.119

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.3

(source)

DANN

Benign

0.76

PhyloP100

-0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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