Genetic Variant FGFR1OP2:c.511-328C>T (chr12-26963014-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.405

Publications

2 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FGFR1OP2	NM_015633.3 link	c.511-328C>T		intron_variant	Intron 5 of 6	ENST00000229395.8	NP_056448.1	Q9NVK5-1
FGFR1OP2	NM_001171887.2 link	c.397-328C>T		intron_variant	Intron 4 of 5		NP_001165358.1	Q9NVK5-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FGFR1OP2	ENST00000229395.8 link	c.511-328C>T	intron_variant	Intron 5 of 6	2	NM_015633.3	ENSP00000229395.3	Q9NVK5-1
FGFR1OP2	ENST00000538172.1 link	n.2019C>T	non_coding_transcript_exon_variant	Exon 1 of 2	2
FGFR1OP2	ENST00000327214.5 link	c.397-328C>T	intron_variant	Intron 4 of 5	2		ENSP00000323763.5	Q9NVK5-2

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19139

AN:

151832

Hom.:

1230

Cov.:

show subpopulations

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.:

AF XY:

0.127

AC XY:

1049

AN XY:

8254

show subpopulations

African (AFR)

AF:

0.103

AC:

AN:

632

American (AMR)

AF:

0.0830

AC:

AN:

530

Ashkenazi Jewish (ASJ)

AF:

0.0671

AC:

AN:

656

East Asian (EAS)

AF:

0.00193

AC:

AN:

1036

South Asian (SAS)

AF:

0.164

AC:

AN:

518

European-Finnish (FIN)

AF:

0.143

AC:

AN:

638

Middle Eastern (MID)

AF:

0.0833

AC:

AN:

European-Non Finnish (NFE)

AF:

0.146

AC:

1565

AN:

10746

Other (OTH)

AF:

0.115

AC:

121

AN:

1048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

175

263

350

438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.126

AC:

19148

AN:

151950

Hom.:

1232

Cov.:

AF XY:

0.125

AC XY:

9281

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.0970

AC:

4019

AN:

41438

American (AMR)

AF:

0.104

AC:

1585

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.0833

AC:

288

AN:

3456

East Asian (EAS)

AF:

0.00347

AC:

AN:

5190

South Asian (SAS)

AF:

0.162

AC:

782

AN:

4816

European-Finnish (FIN)

AF:

0.147

AC:

1543

AN:

10526

Middle Eastern (MID)

AF:

0.0616

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.155

AC:

10536

AN:

67954

Other (OTH)

AF:

0.145

AC:

306

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

889

1778

2668

3557

4446

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.140

Hom.:

5535

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

(source)

DANN

Benign

0.75

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over