12-26940652-G-C

Variant names:

• chr12-26940652-G-C
• rs840869
• NM_015633.3:c.-15+1942G>C

Variant summary

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

The NM_015633.3(FGFR1OP2):​c.-15+1942G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,106 control chromosomes in the GnomAD database, including 46,334 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 0.77 (46334 hom., cov: 32)
• Consequence: FGFR1OP2 NM_015633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 3 publications found

Genes affected

FGFR1OP2 (HGNC:23098): (FGFR1 oncogene partner 2) Predicted to enable identical protein binding activity. Predicted to be involved in response to wounding. Predicted to act upstream of or within wound healing. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3	c.-15+1942G>C		intron_variant	Intron 1 of 6	ENST00000229395.8	NP_056448.1
FGFR1OP2	NM_001171887.2	c.-15+1942G>C		intron_variant	Intron 1 of 5		NP_001165358.1
FGFR1OP2	NM_001171888.2	c.-15+1942G>C		intron_variant	Intron 1 of 4		NP_001165359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR1OP2	ENST00000229395.8	c.-15+1942G>C		intron_variant	Intron 1 of 6	2	NM_015633.3	ENSP00000229395.3

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117678 AN: 151988 Hom.: 46291 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.774 AC: 117775 AN: 152106 Hom.: 46334 Cov.: 32 AF XY: 0.775 AC XY: 57660 AN XY: 74360

African (AFR) AF: 0.910 AC: 37777 AN: 41532

American (AMR) AF: 0.679 AC: 10366 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4848 AN: 5186

South Asian (SAS) AF: 0.809 AC: 3891 AN: 4810

European-Finnish (FIN) AF: 0.727 AC: 7674 AN: 10560

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48140 AN: 67970

Other (OTH) AF: 0.746 AC: 1570 AN: 2104

Alfa AF: 0.650 Hom.: 1827

Bravo AF: 0.776

Asia WGS AF: 0.879 AC: 3053 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.72
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs840869; hg19: chr12-27093585;