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

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.

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