2-28391866-CTTTTTT-CTTTTTTTTTTT

Variant names:

• chr2-28391866-C-CTTTTT
• rs4042624
• ENST00000427929.5:n.125+2681_125+2682insAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000427929.5(FOSL2-AS1):​n.125+2681_125+2682insAAAAA variant causes a intron 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: FOSL2-AS1 ENST00000427929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• 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
FOSL2-AS1	ENST00000427929.5	n.125+2681_125+2682insAAAAA		intron_variant	Intron 1 of 1	2
FOSL2-AS1	ENST00000445878.1	n.125+2681_125+2682insAAAAA		intron_variant	Intron 1 of 2	4
FOSL2-AS1	ENST00000688938.1	n.133+2681_133+2682insAAAAA		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.00238

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000310

Gnomad4 OTH AF: 0.00175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4042624; hg19: chr2-28614733;