Genetic Variant ENST00000752769.1:n.744_748delTTTTT (chr2-28391866-CTTTTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000752769.1(ENSG00000298060):n.744_748delTTTTT 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 0.000016 ( 0 hom., cov: 0)

Consequence

ENSG00000298060
ENST00000752769.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139

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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752769.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOSL2-AS1	NR_103831.1		n.125+2677_125+2681delAAAAA		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000298060	ENST00000752769.1		n.744_748delTTTTT	non_coding_transcript_exon	Exon 2 of 2
ENSG00000298060	ENST00000752770.1		n.364_368delTTTTT	non_coding_transcript_exon	Exon 2 of 2
FOSL2-AS1	ENST00000427929.5	TSL:2	n.125+2677_125+2681delAAAAA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000159

AC:

AN:

125642

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000308

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000163

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.0000159

AC:

AN:

125642

Hom.:

Cov.:

AF XY:

0.0000169

AC XY:

AN XY:

59214

show subpopulations

African (AFR)

AF:

0.0000308

AC:

AN:

32518

American (AMR)

AF:

0.00

AC:

AN:

12600

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3242

East Asian (EAS)

AF:

0.00

AC:

AN:

4498

South Asian (SAS)

AF:

0.00

AC:

AN:

3736

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4880

Middle Eastern (MID)

AF:

0.00

AC:

AN:

228

European-Non Finnish (NFE)

AF:

0.0000163

AC:

AN:

61390

Other (OTH)

AF:

0.00

AC:

AN:

1700

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over