rs1051513

Positions:

• chr12-26963014-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015633.3(FGFR1OP2):​c.511-328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 167,826 control chromosomes in the GnomAD database, including 1,384 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 0.13 (1232 hom., cov: 32)
  • Exomes 𝑓: 0.13 (152 hom.)
• Consequence: FGFR1OP2 NM_015633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3	c.511-328C>T		intron_variant		ENST00000229395.8	NP_056448.1
FGFR1OP2	NM_001171887.2	c.397-328C>T		intron_variant			NP_001165358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR1OP2	ENST00000229395.8	c.511-328C>T		intron_variant		2	NM_015633.3	ENSP00000229395
FGFR1OP2	ENST00000327214.5	c.397-328C>T		intron_variant		2		ENSP00000323763	P1
FGFR1OP2	ENST00000538172.1	n.2019C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19139 AN: 151832 Hom.: 1230 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.127 AC: 2023 AN: 15876 Hom.: 152 Cov.: 0 AF XY: 0.127 AC XY: 1049 AN XY: 8254

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.0830

Gnomad4 ASJ exome AF: 0.0671

Gnomad4 EAS exome AF: 0.00193

Gnomad4 SAS exome AF: 0.164

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.115

GnomAD4 genome AF: 0.126 AC: 19148 AN: 151950 Hom.: 1232 Cov.: 32 AF XY: 0.125 AC XY: 9281 AN XY: 74244

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.145

Alfa AF: 0.142 Hom.: 2538

Bravo AF: 0.118

Asia WGS AF: 0.103 AC: 360 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.75

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: rs1051513; hg19: chr12-27115947;