Variant chr14-65006156-C-CTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002028.4(FNTB):c.209+1859_209+1860dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1243 hom., cov: 0)

Exomes 𝑓: 0.069 ( 35 hom. )

Consequence

FNTB
NM_002028.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.672

Variant links:

Genes affected

FNTB (HGNC:3785): (farnesyltransferase, CAAX box, beta) Enables zinc ion binding activity. Contributes to protein farnesyltransferase activity. Involved in protein farnesylation. Part of microtubule associated complex and protein farnesyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

FNTB links:

CHURC1-FNTB (HGNC:):

CHURC1-FNTB links:

MAX (HGNC:6913): (MYC associated factor X) The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Mutations of this gene have been reported to be associated with hereditary pheochromocytoma. A pseudogene of this gene is located on the long arm of chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

MAX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 14-65006156-C-CTT is Benign according to our data. Variant chr14-65006156-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1245444.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FNTB	NM_002028.4 linkuse as main transcript	c.209+1859_209+1860dup		intron_variant		ENST00000246166.3
CHURC1-FNTB	NM_001202559.1 linkuse as main transcript	c.392+1859_392+1860dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
FNTB	ENST00000246166.3 linkuse as main transcript	c.209+1859_209+1860dup	intron_variant	1	NM_002028.4	P1	P49356-1
FNTB	ENST00000555372.5 linkuse as main transcript	n.268+1859_268+1860dup	intron_variant, non_coding_transcript_variant	3
FNTB	ENST00000555742.5 linkuse as main transcript	n.413+1859_413+1860dup	intron_variant, non_coding_transcript_variant	5
MAX	ENST00000341653.6 linkuse as main transcript		downstream_gene_variant	2			P61244-6

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

17149

AN:

133352

Hom.:

1240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0796

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.0752

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.0688

AC:

91967

AN:

1336218

Hom.:

Cov.:

AF XY:

0.0669

AC XY:

44536

AN XY:

665586

show subpopulations

Gnomad4 AFR exome

AF:

0.0355

Gnomad4 AMR exome

AF:

0.0640

Gnomad4 ASJ exome

AF:

0.0328

Gnomad4 EAS exome

AF:

0.0506

Gnomad4 SAS exome

AF:

0.0430

Gnomad4 FIN exome

AF:

0.0531

Gnomad4 NFE exome

AF:

0.0748

Gnomad4 OTH exome

AF:

0.0587

GnomAD4 genome

AF:

0.129

AC:

17157

AN:

133324

Hom.:

1243

Cov.:

AF XY:

0.129

AC XY:

8225

AN XY:

63754

show subpopulations

Gnomad4 AFR

AF:

0.0795

Gnomad4 AMR

AF:

0.185

Gnomad4 ASJ

AF:

0.0956

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.124

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 09, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over