ENST00000752769.1:n.746_748dupTTT

Variant names:

• chr2-28391866-C-CTTT
• rs4042624
• ENST00000752769.1:n.746_748dupTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000752769.1(ENSG00000298060):​n.746_748dupTTT 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 0.34 (8061 hom., cov: 0)
• Consequence: ENSG00000298060 ENST00000752769.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

ENSG00000298060 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOSL2-AS1	NR_103831.1		n.125+2679_125+2681dupAAA		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298060	ENST00000752769.1		n.746_748dupTTT		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298060	ENST00000752770.1		n.366_368dupTTT		non_coding_transcript_exon	Exon 2 of 2
	FOSL2-AS1	ENST00000427929.5	TSL:2	n.125+2679_125+2681dupAAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 42781 AN: 125276 Hom.: 8061 Cov.: 0

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.341 AC: 42774 AN: 125268 Hom.: 8061 Cov.: 0 AF XY: 0.334 AC XY: 19698 AN XY: 59016

African (AFR) AF: 0.250 AC: 8118 AN: 32460

American (AMR) AF: 0.276 AC: 3461 AN: 12558

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 931 AN: 3236

East Asian (EAS) AF: 0.205 AC: 916 AN: 4470

South Asian (SAS) AF: 0.466 AC: 1726 AN: 3700

European-Finnish (FIN) AF: 0.300 AC: 1450 AN: 4830

Middle Eastern (MID) AF: 0.308 AC: 64 AN: 208

European-Non Finnish (NFE) AF: 0.411 AC: 25179 AN: 61248

Other (OTH) AF: 0.323 AC: 552 AN: 1710

Alfa AF: 0.144 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4042624; hg19: chr2-28614733;