Variant 12-26966684-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.254

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]

FGFR1OP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3 link	c.*1951T>G		downstream_gene_variant		ENST00000229395.8	NP_056448.1	Q9NVK5-1
FGFR1OP2	NM_001171887.2 link	c.*1951T>G		downstream_gene_variant			NP_001165358.1	Q9NVK5-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR1OP2	ENST00000229395.8 link	c.*1951T>G		downstream_gene_variant		2	NM_015633.3	ENSP00000229395.3		Q9NVK5-1
FGFR1OP2	ENST00000327214.5 link	c.*1951T>G		downstream_gene_variant		2		ENSP00000323763.5		Q9NVK5-2

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35649

AN:

151872

Hom.:

4490

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.235

AC:

35674

AN:

151990

Hom.:

4494

Cov.:

AF XY:

0.235

AC XY:

17494

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.409

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.187

Hom.:

1355

Bravo

AF:

0.237

Asia WGS

AF:

0.305

AC:

1059

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.2

DANN

Benign

0.73

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over