Variant rs174589 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004265.4(FADS2):c.744+47C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,609,918 control chromosomes in the GnomAD database, including 33,454 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 0.15 ( 2329 hom., cov: 32)

Exomes 𝑓: 0.20 ( 31125 hom. )

Consequence

FADS2
NM_004265.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Variant links:

Genes affected

FADS2 (HGNC:3575): (fatty acid desaturase 2) The protein encoded by this gene is a member of the fatty acid desaturase (FADS) gene family. Desaturase enzymes regulate unsaturation of fatty acids through the introduction of double bonds between defined carbons of the fatty acyl chain. FADS family members are considered fusion products composed of an N-terminal cytochrome b5-like domain and a C-terminal multiple membrane-spanning desaturase portion, both of which are characterized by conserved histidine motifs. This gene is clustered with family members at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

FADS2 links:

LOC124902679 (HGNC:):

LOC124902679 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FADS2	NM_004265.4 linkuse as main transcript	c.744+47C>G		intron_variant		ENST00000278840.9	NP_004256.1	O95864-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FADS2	ENST00000278840.9 linkuse as main transcript	c.744+47C>G		intron_variant		1	NM_004265.4	ENSP00000278840.4		O95864-1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23398

AN:

152000

Hom.:

2332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0458

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.182

GnomAD3 exomes

AF:

0.188

AC:

47248

AN:

250656

Hom.:

5456

AF XY:

0.183

AC XY:

24833

AN XY:

135412

show subpopulations

Gnomad AFR exome

AF:

0.0432

Gnomad AMR exome

AF:

0.354

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.139

Gnomad SAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.134

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.199

AC:

290152

AN:

1457800

Hom.:

31125

Cov.:

AF XY:

0.197

AC XY:

142469

AN XY:

724974

show subpopulations

Gnomad4 AFR exome

AF:

0.0366

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.132

Gnomad4 NFE exome

AF:

0.213

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.154

AC:

23392

AN:

152118

Hom.:

2329

Cov.:

AF XY:

0.151

AC XY:

11225

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0457

Gnomad4 AMR

AF:

0.259

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.115

Hom.:

250

Bravo

AF:

0.159

Asia WGS

AF:

0.150

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.12

DANN

Benign

0.54

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