2-28391927-C-T

Variant names:

• chr2-28391927-C-T
• rs925255
• ENST00000427929.5:n.125+2621G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427929.5(FOSL2-AS1):​n.125+2621G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 147,720 control chromosomes in the GnomAD database, including 11,579 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11579 hom., cov: 26)
• Consequence: FOSL2-AS1 ENST00000427929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOSL2-AS1	NR_103831.1	n.125+2621G>A		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+2621G>A		intron_variant	Intron 1 of 1	2
FOSL2-AS1	ENST00000445878.1	n.125+2621G>A		intron_variant	Intron 1 of 2	4
FOSL2-AS1	ENST00000688938.1	n.133+2621G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 56625 AN: 147638 Hom.: 11581 Cov.: 26

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.383 AC: 56614 AN: 147720 Hom.: 11579 Cov.: 26 AF XY: 0.381 AC XY: 27322 AN XY: 71736

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.363

Alfa AF: 0.436 Hom.: 19297

Bravo AF: 0.370

Asia WGS AF: 0.356 AC: 1233 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.4
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925255; hg19: chr2-28614794;