2-28391534-T-C

Variant names:

• chr2-28391534-T-C
• rs11677002
• ENST00000427929.5:n.125+3014A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427929.5(FOSL2-AS1):​n.125+3014A>G variant causes a intron 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 ENST00000427929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 8 publications found

Genes affected

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

ENSG00000298060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427929.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOSL2-AS1	NR_103831.1		n.125+3014A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOSL2-AS1	ENST00000427929.5	TSL:2	n.125+3014A>G		intron	N/A
	FOSL2-AS1	ENST00000445878.1	TSL:4	n.125+3014A>G		intron	N/A
	FOSL2-AS1	ENST00000688938.2		n.158+3014A>G		intron	N/A

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

African (AFR) AF: 0.276 AC: 11451 AN: 41462

American (AMR) AF: 0.324 AC: 4945 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1221 AN: 5166

South Asian (SAS) AF: 0.505 AC: 2435 AN: 4824

European-Finnish (FIN) AF: 0.454 AC: 4793 AN: 10564

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31278 AN: 67948

Other (OTH) AF: 0.363 AC: 765 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.2
DANN	Benign	0.65
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11677002; hg19: chr2-28614401;