dbSNP rs174620: FADS2:c.883-697A>G (chr11-61862275-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004265.4(FADS2):c.883-697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,098 control chromosomes in the GnomAD database, including 15,635 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 0.44 ( 15610 hom., cov: 31)

Exomes 𝑓: 0.46 ( 25 hom. )

Consequence

FADS2
NM_004265.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250

Publications

10 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004265.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FADS2	NM_004265.4	MANE Select	c.883-697A>G	intron	N/A	NP_004256.1
FADS2	NM_001281501.1		c.817-697A>G	intron	N/A	NP_001268430.1
FADS2	NM_001281502.1		c.790-697A>G	intron	N/A	NP_001268431.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FADS2	ENST00000278840.9	TSL:1 MANE Select	c.883-697A>G	intron	N/A	ENSP00000278840.4
FADS2	ENST00000257261.10	TSL:1	c.817-697A>G	intron	N/A	ENSP00000257261.6
FADS2	ENST00000521849.5	TSL:1	c.883-697A>G	intron	N/A	ENSP00000431091.1

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66615

AN:

151776

Hom.:

15581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.476

Gnomad EAS

AF:

0.0220

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.394

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.460

AC:

AN:

202

Hom.:

Cov.:

AF XY:

0.472

AC XY:

AN XY:

142

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.100

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.471

AC:

AN:

140

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.439

AC:

66691

AN:

151896

Hom.:

15610

Cov.:

AF XY:

0.429

AC XY:

31869

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.549

AC:

22725

AN:

41388

American (AMR)

AF:

0.356

AC:

5445

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

1649

AN:

3466

East Asian (EAS)

AF:

0.0216

AC:

112

AN:

5178

South Asian (SAS)

AF:

0.316

AC:

1523

AN:

4820

European-Finnish (FIN)

AF:

0.394

AC:

4150

AN:

10532

Middle Eastern (MID)

AF:

0.483

AC:

141

AN:

292

European-Non Finnish (NFE)

AF:

0.437

AC:

29651

AN:

67924

Other (OTH)

AF:

0.436

AC:

921

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1881

3762

5642

7523

9404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.438

Hom.:

1860

Bravo

AF:

0.438

Asia WGS

AF:

0.201

AC:

698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.3

(source)

DANN

Benign

0.71

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over