Genetic Variant ENST00000832671.1:n.1393-2259G>T (chr3-168888758-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000832671.1(ENSG00000293389):n.1393-2259G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,178 control chromosomes in the GnomAD database, including 718 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 0.054 ( 718 hom., cov: 32)

Consequence

ENSG00000293389
ENST00000832671.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293389 (HGNC:):

ENSG00000293389 links:

LINC02082 (HGNC:52931): (long intergenic non-protein coding RNA 2082)

LINC02082 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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
ENSG00000293389	ENST00000832671.1 link	n.1393-2259G>T		intron_variant	Intron 10 of 10
LINC02082	ENST00000832792.1 link	n.61-2259G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8227

AN:

152060

Hom.:

713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0187

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.0140

Gnomad SAS

AF:

0.0738

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.000838

Gnomad OTH

AF:

0.0372

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

GnomAD4 genome

AF:

0.0542

AC:

8247

AN:

152178

Hom.:

718

Cov.:

AF XY:

0.0538

AC XY:

4001

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.178

AC:

7369

AN:

41466

American (AMR)

AF:

0.0186

AC:

285

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00749

AC:

AN:

3472

East Asian (EAS)

AF:

0.0141

AC:

AN:

5184

South Asian (SAS)

AF:

0.0728

AC:

351

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000838

AC:

AN:

68020

Other (OTH)

AF:

0.0369

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

344

688

1032

1376

1720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0556

Hom.:

467

Bravo

AF:

0.0602

Asia WGS

AF:

0.0650

AC:

225

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.21

(source)

DANN

Benign

0.73

PhyloP100

-1.4

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