Genetic Variant FDFT1:c.100-57_100-46delCACTCCCACTCC (chr8-11808709-GTCCCACTCCCAC-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP3BP6BA1

The NM_001287750.2(FDFT1):c.220_231delCACTCCCACTCC(p.His74_Ser77del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 1,514,486 control chromosomes in the GnomAD database, including 394 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.030 ( 104 hom., cov: 0)

Exomes 𝑓: 0.017 ( 290 hom. )

Consequence

FDFT1
NM_001287750.2 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

FDFT1 (HGNC:3629): (farnesyl-diphosphate farnesyltransferase 1) This gene encodes a membrane-associated enzyme located at a branch point in the mevalonate pathway. The encoded protein is the first specific enzyme in cholesterol biosynthesis, catalyzing the dimerization of two molecules of farnesyl diphosphate in a two-step reaction to form squalene. [provided by RefSeq, Jul 2008]

FDFT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001287750.2

BP6

Variant 8-11808709-GTCCCACTCCCAC-G is Benign according to our data. Variant chr8-11808709-GTCCCACTCCCAC-G is described in ClinVar as [Benign]. Clinvar id is 3057202.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr8-11808709-GTCCCACTCCCAC-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FDFT1	NM_004462.5 link	c.100-57_100-46delCACTCCCACTCC		intron_variant	Intron 1 of 7	ENST00000220584.9	NP_004453.3	P37268-1Q6IAX1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FDFT1	ENST00000220584.9 link	c.100-57_100-46delCACTCCCACTCC		intron_variant	Intron 1 of 7	1	NM_004462.5	ENSP00000220584.4		P37268-1

Frequencies

GnomAD3 genomes

AF:

0.0300

AC:

4473

AN:

148892

Hom.:

101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0612

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0114

Gnomad ASJ

AF:

0.00492

Gnomad EAS

AF:

0.00564

Gnomad SAS

AF:

0.00494

Gnomad FIN

AF:

0.0584

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.0191

GnomAD4 exome

AF:

0.0173

AC:

23583

AN:

1365482

Hom.:

290

AF XY:

0.0169

AC XY:

11352

AN XY:

672368

show subpopulations

Gnomad4 AFR exome

AF:

0.0651

AC:

2049

AN:

31476

Gnomad4 AMR exome

AF:

0.00849

AC:

298

AN:

35104

Gnomad4 ASJ exome

AF:

0.00733

AC:

172

AN:

23452

Gnomad4 EAS exome

AF:

0.00377

AC:

135

AN:

35816

Gnomad4 SAS exome

AF:

0.00643

AC:

488

AN:

75894

Gnomad4 FIN exome

AF:

0.0528

AC:

2102

AN:

39842

Gnomad4 NFE exome

AF:

0.0163

AC:

17340

AN:

1061300

Gnomad4 Remaining exome

AF:

0.0164

AC:

936

AN:

57030

Heterozygous variant carriers

1294

2588

3883

5177

6471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

666

1332

1998

2664

3330

<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:

0.0302

AC:

4496

AN:

149004

Hom.:

104

Cov.:

AF XY:

0.0316

AC XY:

2297

AN XY:

72618

show subpopulations

Gnomad4 AFR

AF:

0.0616

AC:

0.0616123

AN:

0.0616123

Gnomad4 AMR

AF:

0.0113

AC:

0.011338

AN:

0.011338

Gnomad4 ASJ

AF:

0.00492

AC:

0.00491898

AN:

0.00491898

Gnomad4 EAS

AF:

0.00565

AC:

0.00565428

AN:

0.00565428

Gnomad4 SAS

AF:

0.00473

AC:

0.00472712

AN:

0.00472712

Gnomad4 FIN

AF:

0.0584

AC:

0.0584062

AN:

0.0584062

Gnomad4 NFE

AF:

0.0171

AC:

0.0170693

AN:

0.0170693

Gnomad4 OTH

AF:

0.0189

AC:

0.0188588

AN:

0.0188588

Heterozygous variant carriers

206

411

617

822

1028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0232

Hom.:

2006

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FDFT1-related disorder

Benign:1

Dec 05, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism

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