Genetic Variant ENST00000599841.1:n.25-567_25-566delAC (chr16-86197744-CGT-C) – 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.25-567_25-566delAC 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 0.16 ( 1972 hom., cov: 0)

Consequence

ENSG00000268505
ENST00000599841.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.806

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 (SAS) allele frequency at 95% confidence interval = 0.234 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+1362delGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1 link	n.628-567_628-566delAC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000268505	ENST00000599841.1 link	n.25-567_25-566delAC	intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1 link	n.232+1333_232+1334delGT	intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3 link	n.508+1333_508+1334delGT	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

23564

AN:

147528

Hom.:

1964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.0920

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.160

AC:

23608

AN:

147634

Hom.:

1972

Cov.:

AF XY:

0.159

AC XY:

11418

AN XY:

71816

show subpopulations

African (AFR)

AF:

0.210

AC:

8327

AN:

39708

American (AMR)

AF:

0.177

AC:

2649

AN:

14952

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

387

AN:

3426

East Asian (EAS)

AF:

0.159

AC:

791

AN:

4970

South Asian (SAS)

AF:

0.246

AC:

1121

AN:

4552

European-Finnish (FIN)

AF:

0.0920

AC:

903

AN:

9814

Middle Eastern (MID)

AF:

0.158

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.132

AC:

8870

AN:

66994

Other (OTH)

AF:

0.166

AC:

337

AN:

2028

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

930

1859

2789

3718

4648

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.0648

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.81

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