Genetic Variant FDFT1:c.100-51_100-46dupCACTCC (chr8-11808709-G-GTCCCAC) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_001287750.2(FDFT1):c.226_231dupCACTCC(p.His76_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 0.0011 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00090 ( 8 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 Likely_benign. Variant got -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001287750.2

BS2

High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FDFT1	NM_004462.5 link	c.100-51_100-46dupCACTCC		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.100-51_100-46dupCACTCC		intron_variant	Intron 1 of 7	1	NM_004462.5	ENSP00000220584.4		P37268-1

Frequencies

GnomAD3 genomes

AF:

0.00105

AC:

157

AN:

148920

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00133

Gnomad ASJ

AF:

0.000868

Gnomad EAS

AF:

0.00121

Gnomad SAS

AF:

0.000859

Gnomad FIN

AF:

0.000971

Gnomad MID

AF:

0.00641

Gnomad NFE

AF:

0.000802

Gnomad OTH

AF:

0.00147

GnomAD4 exome

AF:

0.000901

AC:

1231

AN:

1366036

Hom.:

Cov.:

AF XY:

0.000905

AC XY:

609

AN XY:

672636

show subpopulations

Gnomad4 AFR exome

AF:

0.00159

Gnomad4 AMR exome

AF:

0.00450

Gnomad4 ASJ exome

AF:

0.000298

Gnomad4 EAS exome

AF:

0.00513

Gnomad4 SAS exome

AF:

0.000658

Gnomad4 FIN exome

AF:

0.00128

Gnomad4 NFE exome

AF:

0.000605

Gnomad4 OTH exome

AF:

0.00138

GnomAD4 genome

AF:

0.00106

AC:

158

AN:

149032

Hom.:

Cov.:

AF XY:

0.00107

AC XY:

AN XY:

72636

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00139

Gnomad4 ASJ

AF:

0.000868

Gnomad4 EAS

AF:

0.00121

Gnomad4 SAS

AF:

0.000859

Gnomad4 FIN

AF:

0.000971

Gnomad4 NFE

AF:

0.000802

Gnomad4 OTH

AF:

0.00145

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-GTCCCACTCCCACTCCCACTCCCACTCCCACTCCCAC

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