rs11677002

Positions:

• chr2-28391534-T-C

Variant summary

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

The NR_103831.1(FOSL2-AS1):​n.125+3014A>G 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 0.386 in 152,026 control chromosomes in the GnomAD database, including 12,011 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 0.39 (12011 hom., cov: 32)
• Consequence: FOSL2-AS1 NR_103831.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

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=-0.79).
• 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/exons	MANE	Protein	UniProt
FOSL2-AS1	NR_103831.1	n.125+3014A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOSL2-AS1	ENST00000445878.1	n.125+3014A>G		intron_variant, non_coding_transcript_variant		4
FOSL2-AS1	ENST00000427929.5	n.125+3014A>G		intron_variant, non_coding_transcript_variant		2
FOSL2-AS1	ENST00000688938.1	n.133+3014A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58691 AN: 151908 Hom.: 12012 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.386 AC: 58695 AN: 152026 Hom.: 12011 Cov.: 32 AF XY: 0.385 AC XY: 28600 AN XY: 74314

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.363

Alfa AF: 0.417 Hom.: 1717

Bravo AF: 0.370

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11677002; hg19: chr2-28614401;