ENST00000379619.5:c.432G>A
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000379619.5(FOSL2):c.432G>A(p.Pro144Pro) variant causes a synonymous 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. 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
ENST00000379619.5 synonymous
ENST00000379619.5 synonymous
Scores
2
Splicing: ADA: 0.00002265
2
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP7
Synonymous conserved (PhyloP=-1.23 with no splicing effect.
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOSL2 | NM_005253.4 | c.463-7G>A | splice_region_variant, intron_variant | Intron 3 of 3 | ENST00000264716.9 | NP_005244.1 | ||
FOSL2 | XM_006711976.4 | c.507G>A | p.Pro169Pro | synonymous_variant | Exon 4 of 4 | XP_006712039.1 | ||
FOSL2 | XM_006711977.4 | c.390G>A | p.Pro130Pro | synonymous_variant | Exon 4 of 4 | XP_006712040.1 | ||
FOSL2 | XM_005264231.5 | c.566-7G>A | splice_region_variant, intron_variant | Intron 4 of 4 | XP_005264288.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOSL2 | ENST00000379619.5 | c.432G>A | p.Pro144Pro | synonymous_variant | Exon 4 of 4 | 1 | ENSP00000368939.1 | |||
FOSL2 | ENST00000264716.9 | c.463-7G>A | splice_region_variant, intron_variant | Intron 3 of 3 | 1 | NM_005253.4 | ENSP00000264716.4 | |||
FOSL2 | ENST00000436647.1 | c.346-7G>A | splice_region_variant, intron_variant | Intron 3 of 3 | 2 | ENSP00000396497.1 |
Frequencies
GnomAD3 genomes AF: 0.345 AC: 52385AN: 152014Hom.: 9646 Cov.: 32
GnomAD3 genomes
AF:
AC:
52385
AN:
152014
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.360 AC: 89691AN: 249356Hom.: 17174 AF XY: 0.373 AC XY: 50459AN XY: 135158
GnomAD3 exomes
AF:
AC:
89691
AN:
249356
Hom.:
AF XY:
AC XY:
50459
AN XY:
135158
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.408 AC: 596040AN: 1461270Hom.: 124871 Cov.: 41 AF XY: 0.410 AC XY: 297840AN XY: 726958
GnomAD4 exome
AF:
AC:
596040
AN:
1461270
Hom.:
Cov.:
41
AF XY:
AC XY:
297840
AN XY:
726958
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.344 AC: 52386AN: 152132Hom.: 9639 Cov.: 32 AF XY: 0.343 AC XY: 25508AN XY: 74376
GnomAD4 genome
AF:
AC:
52386
AN:
152132
Hom.:
Cov.:
32
AF XY:
AC XY:
25508
AN XY:
74376
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1057
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at