2-28391866-CTTTTTT-CTTTTTTTT

Variant names:

• chr2-28391866-C-CTT
• rs4042624
• ENST00000752769.1:n.747_748dupTT

Variant summary

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

The ENST00000752769.1(ENSG00000298060):​n.747_748dupTT 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 0.14 (2241 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 (AFR) allele frequency at 95% confidence interval = 0.328 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOSL2-AS1	NR_103831.1		n.125+2680_125+2681dupAA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298060	ENST00000752769.1		n.747_748dupTT		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298060	ENST00000752770.1		n.367_368dupTT		non_coding_transcript_exon	Exon 2 of 2
	FOSL2-AS1	ENST00000427929.5	TSL:2	n.125+2680_125+2681dupAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 17503 AN: 125532 Hom.: 2236 Cov.: 0

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0565

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.139 AC: 17504 AN: 125524 Hom.: 2241 Cov.: 0 AF XY: 0.142 AC XY: 8403 AN XY: 59182

African (AFR) AF: 0.333 AC: 10816 AN: 32494

American (AMR) AF: 0.0911 AC: 1148 AN: 12596

Ashkenazi Jewish (ASJ) AF: 0.0497 AC: 161 AN: 3242

East Asian (EAS) AF: 0.0570 AC: 256 AN: 4488

South Asian (SAS) AF: 0.120 AC: 445 AN: 3704

European-Finnish (FIN) AF: 0.0790 AC: 385 AN: 4874

Middle Eastern (MID) AF: 0.0769 AC: 16 AN: 208

European-Non Finnish (NFE) AF: 0.0655 AC: 4021 AN: 61356

Other (OTH) AF: 0.121 AC: 208 AN: 1712

Alfa AF: 0.0266 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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;