12-26966684-T-G

Variant names:

• chr12-26966684-T-G
• rs2129091
• NM_015633.3:c.*1951T>G

Variant summary

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

The NM_015633.3(FGFR1OP2):​c.*1951T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,990 control chromosomes in the GnomAD database, including 4,494 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 0.23 (4494 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: FGFR1OP2 NM_015633.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015633.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGFR1OP2	NM_015633.3	MANE Select	c.*1951T>G		downstream_gene	N/A	NP_056448.1
	FGFR1OP2	NM_001171887.2		c.*1951T>G		downstream_gene	N/A	NP_001165358.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGFR1OP2	ENST00000229395.8	TSL:2 MANE Select	c.*1951T>G		downstream_gene	N/A	ENSP00000229395.3
	FGFR1OP2	ENST00000327214.5	TSL:2	c.*1951T>G		downstream_gene	N/A	ENSP00000323763.5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35649 AN: 151872 Hom.: 4490 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.217

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.235 AC: 35674 AN: 151990 Hom.: 4494 Cov.: 31 AF XY: 0.235 AC XY: 17494 AN XY: 74294

African (AFR) AF: 0.289 AC: 11982 AN: 41438

American (AMR) AF: 0.206 AC: 3144 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2117 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4824

European-Finnish (FIN) AF: 0.223 AC: 2349 AN: 10544

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13235 AN: 67960

Other (OTH) AF: 0.220 AC: 465 AN: 2114

Alfa AF: 0.190 Hom.: 1558

Bravo AF: 0.237

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		-0.25
Mutation Taster		=98/2	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2129091; hg19: chr12-27119617;