rs12624279

chr2-28411923-G-Achr2-28411923-G-Cchr2-28411923-G-T

Variant summary

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

The NM_005253.4(FOSL2):c.463-7G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 1,613,402 control chromosomes in the GnomAD database, including 134,510 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (9639 hom., cov: 32)
  • Exomes 𝑓: 0.41 (124871 hom.)
• Consequence: FOSL2 NM_005253.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.00002265
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

FOSL2 (HGNC:3798): (FOS like 2, AP-1 transcription factor subunit) The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOSL2	NM_005253.4	c.463-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000264716.9
FOSL2	XM_006711976.4	c.507G>A	p.Pro169=	synonymous_variant	4/4
FOSL2	XM_006711977.4	c.390G>A	p.Pro130=	synonymous_variant	4/4
FOSL2	XM_005264231.5	c.566-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOSL2	ENST00000379619.5	c.432G>A	p.Pro144=	synonymous_variant	4/4	1
FOSL2	ENST00000264716.9	c.463-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_005253.4	P1
FOSL2	ENST00000436647.1	c.346-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52385 AN: 152014 Hom.: 9646 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.317

GnomAD3 exomes AF: 0.360 AC: 89691 AN: 249356 Hom.: 17174 AF XY: 0.373 AC XY: 50459 AN XY: 135158

Gnomad AFR exome AF: 0.241

Gnomad AMR exome AF: 0.256

Gnomad ASJ exome AF: 0.283

Gnomad EAS exome AF: 0.189

Gnomad SAS exome AF: 0.467

Gnomad FIN exome AF: 0.411

Gnomad NFE exome AF: 0.404

Gnomad OTH exome AF: 0.368

GnomAD4 exome AF: 0.408 AC: 596040 AN: 1461270 Hom.: 124871 Cov.: 41 AF XY: 0.410 AC XY: 297840 AN XY: 726958

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.290

Gnomad4 EAS exome AF: 0.188

Gnomad4 SAS exome AF: 0.467

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.385

GnomAD4 genome AF: 0.344 AC: 52386 AN: 152132 Hom.: 9639 Cov.: 32 AF XY: 0.343 AC XY: 25508 AN XY: 74376

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.318

Alfa AF: 0.384 Hom.: 26828

Bravo AF: 0.328

Asia WGS AF: 0.304 AC: 1057 AN: 3478

EpiCase AF: 0.389

EpiControl AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.4
Dann	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000023
dbscSNV1_RF	Benign	0.0020
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12624279; hg19: chr2-28634790; COSMIC: COSV53104684; COSMIC: COSV53104684;