8-11808709-GTCCCACTCCCACTCCCACTCCCACTCCCAC-GTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCACTCCCAC

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3

The NM_001287750.2(FDFT1):​c.196_231dupCACTCCCACTCCCACTCCCACTCCCACTCCCACTCC​(p.His66_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: đť‘“ 0.00016 ( 0 hom., cov: 0)
Exomes đť‘“: 0.00010 ( 3 hom. )
Failed GnomAD Quality Control

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001287750.2

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FDFT1NM_004462.5 linkc.100-81_100-46dupCACTCCCACTCCCACTCCCACTCCCACTCCCACTCC 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
FDFT1ENST00000220584.9 linkc.100-81_100-46dupCACTCCCACTCCCACTCCCACTCCCACTCCCACTCC intron_variant Intron 1 of 7 1 NM_004462.5 ENSP00000220584.4 P37268-1

Frequencies

GnomAD3 genomes
AF:
0.000161
AC:
24
AN:
148922
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.0155
Gnomad AMR
AF:
0.000199
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000429
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000743
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000102
AC:
140
AN:
1366052
Hom.:
3
Cov.:
0
AF XY:
0.000141
AC XY:
95
AN XY:
672638
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000114
Gnomad4 ASJ exome
AF:
0.0000426
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00120
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000292
Gnomad4 OTH exome
AF:
0.000175
GnomAD4 genome
AF:
0.000161
AC:
24
AN:
148922
Hom.:
0
Cov.:
0
AF XY:
0.000124
AC XY:
9
AN XY:
72512
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000199
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000429
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000743
Gnomad4 OTH
AF:
0.00

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.

Other links and lift over

dbSNP: rs71711801; hg19: chr8-11666218; API