Variant chr8-11802542-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001287742.2(FDFT1):c.-75+87A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 35)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FDFT1
NM_001287742.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.516

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:

ENSG00000255046 (HGNC:):

ENSG00000255046 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
FDFT1	NM_001287742.2 linkuse as main transcript	c.-75+87A>T	intron_variant	NP_001274671.1	P37268-1Q6IAX1
FDFT1	NM_001287743.2 linkuse as main transcript	c.-74-217A>T	intron_variant	NP_001274672.1	P37268-1Q6IAX1
FDFT1	NM_001287744.2 linkuse as main transcript	c.-93-6252A>T	intron_variant	NP_001274673.1	P37268-2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
FDFT1	ENST00000530337.6 linkuse as main transcript	c.-75+87A>T	intron_variant		3	ENSP00000431852.2	E9PJG4
FDFT1	ENST00000615631.4 linkuse as main transcript	c.-74-217A>T	intron_variant		5	ENSP00000481481.1	P37268-1
ENSG00000255046	ENST00000533405.1 linkuse as main transcript	n.27T>A	non_coding_transcript_exon_variant	1/2	3
ENSG00000255046	ENST00000531395.1 linkuse as main transcript	n.-30T>A	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

416248

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

229320

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

7.9

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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