Variant rs62078748 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004104.5(FASN):c.-8+672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,344 control chromosomes in the GnomAD database, including 5,118 homozygotes. 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: 𝑓 0.24 ( 5114 hom., cov: 35)

Exomes 𝑓: 0.35 ( 4 hom. )

Consequence

FASN
NM_004104.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0610

Variant links:

Genes affected

FASN (HGNC:3594): (fatty acid synthase) The enzyme encoded by this gene is a multifunctional protein. Its main function is to catalyze the synthesis of palmitate from acetyl-CoA and malonyl-CoA, in the presence of NADPH, into long-chain saturated fatty acids. In some cancer cell lines, this protein has been found to be fused with estrogen receptor-alpha (ER-alpha), in which the N-terminus of FAS is fused in-frame with the C-terminus of ER-alpha. [provided by RefSeq, Jul 2008]

FASN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FASN	NM_004104.5 linkuse as main transcript	c.-8+672G>A		intron_variant		ENST00000306749.4
FASN	XM_011523538.3 linkuse as main transcript	c.-3+672G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FASN	ENST00000306749.4 linkuse as main transcript	c.-8+672G>A		intron_variant		1	NM_004104.5	P1

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36402

AN:

152144

Hom.:

5115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.0639

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.251

GnomAD4 exome

AF:

0.345

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.346

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.239

AC:

36400

AN:

152260

Hom.:

5114

Cov.:

AF XY:

0.238

AC XY:

17743

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.211

Gnomad4 EAS

AF:

0.0643

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.323

Gnomad4 OTH

AF:

0.248

Alfa

AF:

0.281

Hom.:

795

Bravo

AF:

0.225

Asia WGS

AF:

0.113

AC:

394

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.4

DANN

Benign

0.91

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