Genetic Variant ENSG00000268505:n.25-566_25-565insACAC (chr16-86197744-C-CGTGT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000599841.1(ENSG00000268505):n.25-566_25-565insACAC 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 0.0047 ( 4 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01082	NR_103859.1 link	n.232+1359_232+1362dupGTGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1 link	n.628-569_628-566dupACAC		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.00469

AC:

693

AN:

147852

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00616

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00281

Gnomad ASJ

AF:

0.000292

Gnomad EAS

AF:

0.00140

Gnomad SAS

AF:

0.00986

Gnomad FIN

AF:

0.00513

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00441

Gnomad OTH

AF:

0.00348

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

GnomAD4 genome

AF:

0.00468

AC:

693

AN:

147958

Hom.:

Cov.:

AF XY:

0.00472

AC XY:

340

AN XY:

71980

show subpopulations

African (AFR)

AF:

0.00614

AC:

244

AN:

39742

American (AMR)

AF:

0.00281

AC:

AN:

14968

Ashkenazi Jewish (ASJ)

AF:

0.000292

AC:

AN:

3430

East Asian (EAS)

AF:

0.00141

AC:

AN:

4976

South Asian (SAS)

AF:

0.00987

AC:

AN:

4558

European-Finnish (FIN)

AF:

0.00513

AC:

AN:

9946

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00441

AC:

296

AN:

67114

Other (OTH)

AF:

0.00344

AC:

AN:

2032

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

114

143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00361

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-CGTGTGTGTGTGTGTGTGTGTGT

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