Genetic Variant LINC01010:n.54-25919T>G (chr6-134411396-T-G) – 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.54-25919T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,144 control chromosomes in the GnomAD database, including 14,778 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 0.34 ( 14778 hom., cov: 32)

Consequence

LINC01010
ENST00000431422.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307

Publications

2 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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.54-25919T>G		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1 link	n.54-53345T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51911

AN:

152026

Hom.:

14730

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.342

AC:

52001

AN:

152144

Hom.:

14778

Cov.:

AF XY:

0.333

AC XY:

24749

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.781

AC:

32390

AN:

41470

American (AMR)

AF:

0.224

AC:

3418

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1183

AN:

3472

East Asian (EAS)

AF:

0.158

AC:

818

AN:

5176

South Asian (SAS)

AF:

0.176

AC:

848

AN:

4826

European-Finnish (FIN)

AF:

0.102

AC:

1085

AN:

10602

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11100

AN:

67994

Other (OTH)

AF:

0.347

AC:

732

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1183

2366

3548

4731

5914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.236

Hom.:

7562

Bravo

AF:

0.372

Asia WGS

AF:

0.186

AC:

648

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

3.0

(source)

DANN

Benign

0.52

PhyloP100

-0.31

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