rs374120316

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_015033.3(FNBP1):c.1194A>G(p.Thr398Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000257 in 1,609,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000099 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00027 ( 0 hom. )

Consequence

FNBP1
NM_015033.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.25

Publications

2 publications found

Variant links:

Genes affected

FNBP1 (HGNC:17069): (formin binding protein 1) The protein encoded by this gene is a member of the formin-binding-protein family. The protein contains an N-terminal Fer/Cdc42-interacting protein 4 (CIP4) homology (FCH) domain followed by a coiled-coil domain, a proline-rich motif, a second coiled-coil domain, a Rho family protein-binding domain (RBD), and a C-terminal SH3 domain. This protein binds sorting nexin 2 (SNX2), tankyrase (TNKS), and dynamin; an interaction between this protein and formin has not been demonstrated yet in human. [provided by RefSeq, Jul 2008]

FNBP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.027).

BP6

Variant 9-129908991-T-C is Benign according to our data. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-129908991-T-C is described in CliVar as Likely_benign. Clinvar id is 2659579.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.25 with no splicing effect.

BS2

High AC in GnomAd4 at 15 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNBP1	NM_015033.3 link	c.1194A>G	p.Thr398Thr	synonymous_variant	Exon 12 of 17	ENST00000446176.7	NP_055848.1	Q96RU3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNBP1	ENST00000446176.7 link	c.1194A>G	p.Thr398Thr	synonymous_variant	Exon 12 of 17	1	NM_015033.3	ENSP00000413625.1		Q96RU3-1

Frequencies

GnomAD3 genomes

AF:

0.0000986

AC:

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000885

AC:

AN:

248530

AF XY:

0.0000815

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000195

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000273

AC:

398

AN:

1457514

Hom.:

Cov.:

AF XY:

0.000251

AC XY:

182

AN XY:

725374

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33390

American (AMR)

AF:

0.00

AC:

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26100

East Asian (EAS)

AF:

0.00

AC:

AN:

39680

South Asian (SAS)

AF:

0.00

AC:

AN:

86164

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53216

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5760

European-Non Finnish (NFE)

AF:

0.000338

AC:

375

AN:

1108286

Other (OTH)

AF:

0.000382

AC:

AN:

60224

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000986

AC:

AN:

152192

Hom.:

Cov.:

AF XY:

0.0000672

AC XY:

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0000724

AC:

AN:

41448

American (AMR)

AF:

0.00

AC:

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5202

South Asian (SAS)

AF:

0.00

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000176

AC:

AN:

68036

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000315

Hom.:

Bravo

AF:

0.000117

EpiCase

AF:

0.000109

EpiControl

AF:

0.000178

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Sep 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

FNBP1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.071

(source)

DANN

Benign

0.36

PhyloP100

-4.3

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over