Genetic Variant ENSG00000268505:n.25-566_25-565insAC (chr16-86197744-C-CGT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000599841.1(ENSG00000268505):n.25-566_25-565insAC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.072 ( 413 hom., cov: 0)

Consequence

ENSG00000268505
ENST00000599841.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

1 publications found

Variant links:

Genes affected

ENSG00000268505 (HGNC:):

ENSG00000268505 links:

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

LINC01082 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01082	NR_103859.1 link	n.232+1361_232+1362dupGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1 link	n.628-567_628-566dupAC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000268505	ENST00000599841.1 link	n.25-566_25-565insAC	intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1 link	n.232+1332_232+1333insGT	intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3 link	n.508+1332_508+1333insGT	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0717

AC:

10598

AN:

147802

Hom.:

412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0934

Gnomad AMI

AF:

0.0744

Gnomad AMR

AF:

0.0536

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.0309

Gnomad SAS

AF:

0.0537

Gnomad FIN

AF:

0.0351

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0740

Gnomad OTH

AF:

0.0642

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

GnomAD4 genome

AF:

0.0717

AC:

10605

AN:

147906

Hom.:

413

Cov.:

AF XY:

0.0683

AC XY:

4913

AN XY:

71946

show subpopulations

African (AFR)

AF:

0.0934

AC:

3709

AN:

39720

American (AMR)

AF:

0.0535

AC:

800

AN:

14962

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

169

AN:

3430

East Asian (EAS)

AF:

0.0305

AC:

152

AN:

4976

South Asian (SAS)

AF:

0.0540

AC:

246

AN:

4558

European-Finnish (FIN)

AF:

0.0351

AC:

349

AN:

9946

Middle Eastern (MID)

AF:

0.0582

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0740

AC:

4964

AN:

67092

Other (OTH)

AF:

0.0650

AC:

132

AN:

2030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

465

931

1396

1862

2327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0431

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.1

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.

16-86197744-CGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGTGTGT

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