rs859024

Variant names:

• chr12-26949924-A-G
• rs859024
• NM_015633.3:c.-14-4221A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-26949924-A-G
• chr12-26949924-A-T

Variant summary

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

The NM_015633.3(FGFR1OP2):​c.-14-4221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,084 control chromosomes in the GnomAD database, including 58,304 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 0.87 (58304 hom., cov: 30)
• Consequence: FGFR1OP2 NM_015633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3	c.-14-4221A>G		intron_variant	Intron 1 of 6	ENST00000229395.8	NP_056448.1
FGFR1OP2	NM_001171887.2	c.-14-4221A>G		intron_variant	Intron 1 of 5		NP_001165358.1
FGFR1OP2	NM_001171888.2	c.-14-4221A>G		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.-14-4221A>G		intron_variant	Intron 1 of 6	2	NM_015633.3	ENSP00000229395.3

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132614 AN: 151966 Hom.: 58242 Cov.: 30

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.873 AC: 132736 AN: 152084 Hom.: 58304 Cov.: 30 AF XY: 0.876 AC XY: 65113 AN XY: 74354

African (AFR) AF: 0.964 AC: 39996 AN: 41494

American (AMR) AF: 0.889 AC: 13578 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2836 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5174

South Asian (SAS) AF: 0.894 AC: 4303 AN: 4812

European-Finnish (FIN) AF: 0.837 AC: 8847 AN: 10568

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55124 AN: 67984

Other (OTH) AF: 0.870 AC: 1833 AN: 2106

Alfa AF: 0.825 Hom.: 25011

Bravo AF: 0.881

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.60
PhyloP100		-1.0
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: rs859024; hg19: chr12-27102857;