12-26940652-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
FGFR1OP2NM_015633.3 linkuse as main transcriptc.-15+1942G>C intron_variant ENST00000229395.8
FGFR1OP2NM_001171887.2 linkuse as main transcriptc.-15+1942G>C intron_variant
FGFR1OP2NM_001171888.2 linkuse as main transcriptc.-15+1942G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGFR1OP2ENST00000229395.8 linkuse as main transcriptc.-15+1942G>C intron_variant 2 NM_015633.3 Q9NVK5-1

Frequencies

GnomAD3 genomes
AF:
0.774
AC:
117678
AN:
151988
Hom.:
46291
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.910
Gnomad4 AMR
AF:
0.679
Gnomad4 ASJ
AF:
0.737
Gnomad4 EAS
AF:
0.935
Gnomad4 SAS
AF:
0.809
Gnomad4 FIN
AF:
0.727
Gnomad4 NFE
AF:
0.708
Gnomad4 OTH
AF:
0.746
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs840869; hg19: chr12-27093585; API