Genetic Variant FDFT1:c.100-57_100-46dupCACTCCCACTCC (chr8-11808709-G-GTCCCACTCCCAC) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3BA1

The NM_001287750.2(FDFT1):c.220_231dupCACTCCCACTCC(p.His74_Ser77dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.015 ( 39 hom., cov: 0)

Exomes 𝑓: 0.014 ( 282 hom. )

Consequence

FDFT1
NM_001287750.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

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 made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001287750.2

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.086 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_100-46dupCACTCCCACTCC		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_100-46dupCACTCCCACTCC		intron_variant	Intron 1 of 7	1	NM_004462.5	ENSP00000220584.4		P37268-1

Frequencies

GnomAD3 genomes

AF:

0.0146

AC:

2180

AN:

148906

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00557

Gnomad AMI

AF:

0.00773

Gnomad AMR

AF:

0.0477

Gnomad ASJ

AF:

0.0188

Gnomad EAS

AF:

0.0155

Gnomad SAS

AF:

0.00837

Gnomad FIN

AF:

0.0165

Gnomad MID

AF:

0.00641

Gnomad NFE

AF:

0.0125

Gnomad OTH

AF:

0.0171

GnomAD4 exome

AF:

0.0142

AC:

19353

AN:

1366006

Hom.:

282

Cov.:

AF XY:

0.0136

AC XY:

9115

AN XY:

672620

show subpopulations

Gnomad4 AFR exome

AF:

0.00486

Gnomad4 AMR exome

AF:

0.0886

Gnomad4 ASJ exome

AF:

0.0179

Gnomad4 EAS exome

AF:

0.0194

Gnomad4 SAS exome

AF:

0.00689

Gnomad4 FIN exome

AF:

0.0125

Gnomad4 NFE exome

AF:

0.0122

Gnomad4 OTH exome

AF:

0.0166

GnomAD4 genome

AF:

0.0147

AC:

2184

AN:

149018

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

1136

AN XY:

72628

show subpopulations

Gnomad4 AFR

AF:

0.00557

Gnomad4 AMR

AF:

0.0479

Gnomad4 ASJ

AF:

0.0188

Gnomad4 EAS

AF:

0.0155

Gnomad4 SAS

AF:

0.00838

Gnomad4 FIN

AF:

0.0165

Gnomad4 NFE

AF:

0.0125

Gnomad4 OTH

AF:

0.0169

ClinVar

Not reported in ClinVar

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.

8-11808709-GTCCCACTCCCACTCCCACTCCCACTCCCAC-GTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCAC

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