rs1876774

Variant names:

• chr2-28392174-C-G
• rs1876774
• ENST00000427929.5:n.125+2374G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-28392174-C-G
• chr2-28392174-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000427929.5(FOSL2-AS1):​n.125+2374G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00557 in 146,884 control chromosomes in the GnomAD database, including 7 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 0.0056 (7 hom., cov: 31)
• Consequence: FOSL2-AS1 ENST00000427929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 1 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=-0.49).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00557 (818/146884) while in subpopulation AFR AF = 0.0188 (771/40974). AF 95% confidence interval is 0.0177. There are 7 homozygotes in GnomAd4. There are 387 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOSL2-AS1	NR_103831.1	n.125+2374G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOSL2-AS1	ENST00000427929.5	n.125+2374G>C		intron_variant	Intron 1 of 1	2
FOSL2-AS1	ENST00000445878.1	n.125+2374G>C		intron_variant	Intron 1 of 2	4
FOSL2-AS1	ENST00000688938.2	n.158+2374G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00550 AC: 808 AN: 146778 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00277

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: 0.0000151

Gnomad OTH AF: 0.00247

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

GnomAD4 genome AF: 0.00557 AC: 818 AN: 146884 Hom.: 7 Cov.: 31 AF XY: 0.00541 AC XY: 387 AN XY: 71574

African (AFR) AF: 0.0188 AC: 771 AN: 40974

American (AMR) AF: 0.00277 AC: 41 AN: 14812

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3400

East Asian (EAS) AF: 0.00 AC: 0 AN: 5084

South Asian (SAS) AF: 0.00 AC: 0 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8488

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000151 AC: 1 AN: 66070

Other (OTH) AF: 0.00245 AC: 5 AN: 2044

Alfa AF: 0.0000700 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1876774; hg19: chr2-28615041;