2-28391866-CTTTTTT-CTTTTTTTTTTT

Variant names:

• chr2-28391866-C-CTTTTT
• rs4042624
• ENST00000752769.1:n.744_748dupTTTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000752769.1(ENSG00000298060):​n.744_748dupTTTTT 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 0.0047 (8 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0047 (590/125620) while in subpopulation AFR AF = 0.0165 (537/32538). AF 95% confidence interval is 0.0153. There are 8 homozygotes in GnomAd4. There are 274 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298060	ENST00000752769.1	n.744_748dupTTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298060	ENST00000752770.1	n.364_368dupTTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
FOSL2-AS1	ENST00000427929.5	n.125+2677_125+2681dupAAAAA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.00470 AC: 590 AN: 125628 Hom.: 8 Cov.: 0

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00238

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00439

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.00176

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

GnomAD4 genome AF: 0.00470 AC: 590 AN: 125620 Hom.: 8 Cov.: 0 AF XY: 0.00463 AC XY: 274 AN XY: 59224

African (AFR) AF: 0.0165 AC: 537 AN: 32538

American (AMR) AF: 0.00238 AC: 30 AN: 12612

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4488

South Asian (SAS) AF: 0.00 AC: 0 AN: 3712

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

Middle Eastern (MID) AF: 0.00481 AC: 1 AN: 208

European-Non Finnish (NFE) AF: 0.000310 AC: 19 AN: 61378

Other (OTH) AF: 0.00175 AC: 3 AN: 1712

Alfa AF: 0.00 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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;