2-28391866-CTTTTTT-CT

Variant names:

• chr2-28391866-CTTTTT-C
• rs4042624
• ENST00000752769.1:n.744_748delTTTTT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 1 publications found

Genes affected

ENSG00000298060 (HGNC:):

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOSL2-AS1	NR_103831.1	n.125+2677_125+2681delAAAAA		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298060	ENST00000752769.1	n.744_748delTTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298060	ENST00000752770.1	n.364_368delTTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
FOSL2-AS1	ENST00000427929.5	n.125+2677_125+2681delAAAAA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0000159 AC: 2 AN: 125642 Hom.: 0 Cov.: 0

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: 2 AN: 125642 Hom.: 0 Cov.: 0 AF XY: 0.0000169 AC XY: 1 AN XY: 59214

African (AFR) AF: 0.0000308 AC: 1 AN: 32518

American (AMR) AF: 0.00 AC: 0 AN: 12600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3242

East Asian (EAS) AF: 0.00 AC: 0 AN: 4498

South Asian (SAS) AF: 0.00 AC: 0 AN: 3736

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4880

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 228

European-Non Finnish (NFE) AF: 0.0000163 AC: 1 AN: 61390

Other (OTH) AF: 0.00 AC: 0 AN: 1700

Alfa AF: 0.00 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14

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;