2-28391866-CTTTTTT-CTTTTTTTTTT

Variant names:

• chr2-28391866-C-CTTTT
• rs4042624
• ENST00000752769.1:n.745_748dupTTTT

Variant summary

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

The ENST00000752769.1(ENSG00000298060):​n.745_748dupTTTT 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 0.019 (44 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 sas. GnomAd4 allele frequency = 0.0188 (2358/125598) while in subpopulation SAS AF = 0.0288 (107/3712). AF 95% confidence interval is 0.0244. There are 44 homozygotes in GnomAd4. There are 1023 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOSL2-AS1	NR_103831.1	n.125+2678_125+2681dupAAAA		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298060	ENST00000752769.1	n.745_748dupTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298060	ENST00000752770.1	n.365_368dupTTTT		non_coding_transcript_exon_variant	Exon 2 of 2
FOSL2-AS1	ENST00000427929.5	n.125+2678_125+2681dupAAAA		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2360 AN: 125606 Hom.: 44 Cov.: 0

Gnomad AFR AF: 0.00874

Gnomad AMI AF: 0.0988

Gnomad AMR AF: 0.0130

Gnomad ASJ AF: 0.0463

Gnomad EAS AF: 0.00400

Gnomad SAS AF: 0.0289

Gnomad FIN AF: 0.00492

Gnomad MID AF: 0.00877

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0165

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

GnomAD4 genome AF: 0.0188 AC: 2358 AN: 125598 Hom.: 44 Cov.: 0 AF XY: 0.0173 AC XY: 1023 AN XY: 59210

African (AFR) AF: 0.00873 AC: 284 AN: 32544

American (AMR) AF: 0.0130 AC: 164 AN: 12612

Ashkenazi Jewish (ASJ) AF: 0.0463 AC: 150 AN: 3242

East Asian (EAS) AF: 0.00401 AC: 18 AN: 4488

South Asian (SAS) AF: 0.0288 AC: 107 AN: 3712

European-Finnish (FIN) AF: 0.00492 AC: 24 AN: 4880

Middle Eastern (MID) AF: 0.00962 AC: 2 AN: 208

European-Non Finnish (NFE) AF: 0.0244 AC: 1497 AN: 61350

Other (OTH) AF: 0.0164 AC: 28 AN: 1712

Alfa AF: 0.00750 Hom.: 206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16
Mutation Taster		=96/4	polymorphism

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;