2-28391927-C-T

Variant names:

• chr2-28391927-C-T
• rs925255
• ENST00000752769.1:n.792C>T

Variant summary

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

The ENST00000752769.1(ENSG00000298060):​n.792C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 147,720 control chromosomes in the GnomAD database, including 11,579 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 0.38 (11579 hom., cov: 26)
• Consequence: ENSG00000298060 ENST00000752769.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 51 publications found

Genes affected

ENSG00000298060 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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: ENST00000752769.1. 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+2621G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298060	ENST00000752769.1		n.792C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298060	ENST00000752770.1		n.412C>T		non_coding_transcript_exon	Exon 2 of 2
	FOSL2-AS1	ENST00000427929.5	TSL:2	n.125+2621G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 56625 AN: 147638 Hom.: 11581 Cov.: 26

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.383 AC: 56614 AN: 147720 Hom.: 11579 Cov.: 26 AF XY: 0.381 AC XY: 27322 AN XY: 71736

African (AFR) AF: 0.273 AC: 10915 AN: 39986

American (AMR) AF: 0.321 AC: 4800 AN: 14940

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1190 AN: 3448

East Asian (EAS) AF: 0.232 AC: 1179 AN: 5082

South Asian (SAS) AF: 0.505 AC: 2350 AN: 4656

European-Finnish (FIN) AF: 0.429 AC: 3875 AN: 9028

Middle Eastern (MID) AF: 0.326 AC: 94 AN: 288

European-Non Finnish (NFE) AF: 0.460 AC: 30961 AN: 67336

Other (OTH) AF: 0.363 AC: 746 AN: 2056

Alfa AF: 0.423 Hom.: 45645

Bravo AF: 0.370

Asia WGS AF: 0.356 AC: 1233 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.4
DANN	Benign	0.92
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs925255; hg19: chr2-28614794;