8-11808709-G-GTCCCACTCCCACTCCCAC

Position:

• chr8-11808709-G-GTCCCACTCCCACTCCCAC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The ENST00000220584.9(FDFT1):​c.100-63_100-46dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.011 (21 hom., cov: 0)
  • Exomes 𝑓: 0.014 (189 hom.)
• Consequence: FDFT1 ENST00000220584.9 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.258

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 8-11808709-G-GTCCCACTCCCACTCCCAC is Benign according to our data. Variant chr8-11808709-G-GTCCCACTCCCACTCCCAC is described in ClinVar as [Benign]. Clinvar id is 3043487.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FDFT1	NM_004462.5	c.100-63_100-46dup		intron_variant		ENST00000220584.9	NP_004453.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FDFT1	ENST00000220584.9	c.100-63_100-46dup		intron_variant		1	NM_004462.5	ENSP00000220584	P1

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1662 AN: 148918 Hom.: 21 Cov.: 0

Gnomad AFR AF: 0.00321

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0382

Gnomad EAS AF: 0.000201

Gnomad SAS AF: 0.00751

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.0288

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0191

GnomAD4 exome AF: 0.0136 AC: 18632 AN: 1366000 Hom.: 189 Cov.: 0 AF XY: 0.0137 AC XY: 9200 AN XY: 672602

Gnomad4 AFR exome AF: 0.00321

Gnomad4 AMR exome AF: 0.0182

Gnomad4 ASJ exome AF: 0.0331

Gnomad4 EAS exome AF: 0.000279

Gnomad4 SAS exome AF: 0.00849

Gnomad4 FIN exome AF: 0.00329

Gnomad4 NFE exome AF: 0.0142

Gnomad4 OTH exome AF: 0.0157

GnomAD4 genome AF: 0.0112 AC: 1662 AN: 149030 Hom.: 21 Cov.: 0 AF XY: 0.0104 AC XY: 759 AN XY: 72632

Gnomad4 AFR AF: 0.00320

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0382

Gnomad4 EAS AF: 0.000202

Gnomad4 SAS AF: 0.00774

Gnomad4 FIN AF: 0.00340

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0189

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

FDFT1-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 05, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71711801; hg19: chr8-11666218;