Genetic Variant ENST00000599841.1: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

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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