Genetic Variant ENSG00000298060:n.748delT (chr2-28391866-CT-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

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

The ENST00000752769.1(ENSG00000298060):n.748delT variant causes a non coding transcript exon 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 0.0066 ( 4 hom., cov: 0)

Consequence

ENSG00000298060
ENST00000752769.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298060 (HGNC:):

ENSG00000298060 links:

FOSL2-AS1 (HGNC:55784): (FOSL2 antisense RNA 1)

FOSL2-AS1 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
FOSL2-AS1	NR_103831.1 link	n.125+2681delA		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000298060	ENST00000752769.1 link	n.748delT	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298060	ENST00000752770.1 link	n.368delT	non_coding_transcript_exon_variant	Exon 2 of 2
FOSL2-AS1	ENST00000427929.5 link	n.125+2681delA	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.00656

AC:

824

AN:

125626

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00246

Gnomad ASJ

AF:

0.00679

Gnomad EAS

AF:

0.00267

Gnomad SAS

AF:

0.00482

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.00439

Gnomad NFE

AF:

0.00476

Gnomad OTH

AF:

0.00353

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

GnomAD4 genome

AF:

0.00657

AC:

825

AN:

125618

Hom.:

Cov.:

AF XY:

0.00669

AC XY:

396

AN XY:

59216

show subpopulations

African (AFR)

AF:

0.0115

AC:

374

AN:

32548

American (AMR)

AF:

0.00246

AC:

AN:

12612

Ashkenazi Jewish (ASJ)

AF:

0.00679

AC:

AN:

3240

East Asian (EAS)

AF:

0.00267

AC:

AN:

4488

South Asian (SAS)

AF:

0.00485

AC:

AN:

3710

European-Finnish (FIN)

AF:

0.0141

AC:

AN:

4880

Middle Eastern (MID)

AF:

0.00481

AC:

AN:

208

European-Non Finnish (NFE)

AF:

0.00476

AC:

292

AN:

61372

Other (OTH)

AF:

0.00351

AC:

AN:

1710

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

109

145

181

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:

0.00462

Hom.:

206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-28391866-CTTTTTT-CTTTTT

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