Variant 8-11808709-GTCCCACTCCCACTCCCACTCCCACTCCCAC-GTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCAC details in Genebe, Genetics Data Aggregator

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:

Genome browser will be placed here

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.

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