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rs4042624

chr2-28391866-CTTTTT-Cchr2-28391866-CTTTTT-CTchr2-28391866-CTTTTT-CTTchr2-28391866-CTTTTT-CTTTchr2-28391866-CTTTTT-CTTTTchr2-28391866-CTTTTT-CTTTTTTchr2-28391866-CTTTTT-CTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTTTTTchr2-28391866-CTTTTT-CTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NR_103831.1(FOSL2-AS1):n.125+2677_125+2681del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 125,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000016 ( 0 hom., cov: 0)

Consequence

FOSL2-AS1
NR_103831.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139
Variant links:
Genes affected
FOSL2-AS1 (HGNC:55784): (FOSL2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FOSL2-AS1NR_103831.1 linkuse as main transcriptn.125+2677_125+2681del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FOSL2-AS1ENST00000445878.1 linkuse as main transcriptn.125+2677_125+2681del intron_variant, non_coding_transcript_variant 4
FOSL2-AS1ENST00000427929.5 linkuse as main transcriptn.125+2677_125+2681del intron_variant, non_coding_transcript_variant 2
FOSL2-AS1ENST00000688938.1 linkuse as main transcriptn.133+2677_133+2681del intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000159
AC:
2
AN:
125642
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000308
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000163
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0000159
AC:
2
AN:
125642
Hom.:
0
Cov.:
0
AF XY:
0.0000169
AC XY:
1
AN XY:
59214
show subpopulations
Gnomad4 AFR
AF:
0.0000308
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000163
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4042624; hg19: chr2-28614733; API