12-26960581-G-C

Position:

• chr12-26960581-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015633.3(FGFR1OP2):​c.463G>C​(p.Ala155Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FGFR1OP2 NM_015633.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25451243).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3	c.463G>C	p.Ala155Pro	missense_variant	5/7	ENST00000229395.8	NP_056448.1
FGFR1OP2	NM_001171888.2	c.463G>C	p.Ala155Pro	missense_variant	5/5		NP_001165359.1
FGFR1OP2	NM_001171887.2	c.397-2761G>C		intron_variant			NP_001165358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR1OP2	ENST00000229395.8	c.463G>C	p.Ala155Pro	missense_variant	5/7	2	NM_015633.3	ENSP00000229395.3
FGFR1OP2	ENST00000546072.5	c.463G>C	p.Ala155Pro	missense_variant	5/5	1		ENSP00000437556.1
FGFR1OP2	ENST00000327214.5	c.397-2761G>C		intron_variant		2		ENSP00000323763.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Uncertain	0.044	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.031	T;.
Eigen	Benign	-0.15
Eigen_PC	Benign	0.053
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.76	T;T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.25	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-0.98	N;N
REVEL	Benign	0.13
Sift	Benign	0.054	T;D
Sift4G	Benign	0.35	T;T
Polyphen		0.31	B;B
Vest4		0.59
MutPred		0.49		Gain of catalytic residue at A155 (P = 0);Gain of catalytic residue at A155 (P = 0);
MVP		0.30
MPC		0.39
ClinPred		0.87	D
GERP RS		4.3
Varity_R		0.36
gMVP		0.44

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

Other links and lift over

dbSNP: rs11613; hg19: chr12-27113514;