Genetic Variant LINC01010:n.54-24725A>C (chr6-134412590-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000431422.3(LINC01010):n.54-24725A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,148 control chromosomes in the GnomAD database, including 12,912 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 0.32 ( 12912 hom., cov: 32)

Consequence

LINC01010
ENST00000431422.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

Publications

1 publications found

Variant links:

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

LINC01010 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3 link	n.54-24725A>C		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1 link	n.54-52151A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49343

AN:

152030

Hom.:

12881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.335

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

GnomAD4 genome

AF:

0.325

AC:

49413

AN:

152148

Hom.:

12912

Cov.:

AF XY:

0.316

AC XY:

23518

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.723

AC:

29986

AN:

41452

American (AMR)

AF:

0.218

AC:

3332

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1183

AN:

3472

East Asian (EAS)

AF:

0.158

AC:

818

AN:

5174

South Asian (SAS)

AF:

0.174

AC:

839

AN:

4818

European-Finnish (FIN)

AF:

0.102

AC:

1081

AN:

10608

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11053

AN:

68014

Other (OTH)

AF:

0.331

AC:

699

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1216

2432

3648

4864

6080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.245

Hom.:

5745

Bravo

AF:

0.352

Asia WGS

AF:

0.190

AC:

661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.42

(source)

DANN

Benign

0.31

PhyloP100

-2.0

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