dbSNP rs3834458: FADS2:c.142-10329delT (chr11-61827448-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000257261.10(FADS2):c.142-10329delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,130 control chromosomes in the GnomAD database, including 8,063 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 8053 hom., cov: 22)

Exomes 𝑓: 0.37 ( 10 hom. )

Consequence

FADS2
ENST00000257261.10 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.199

Publications

82 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:

FADS1 (HGNC:3574): (fatty acid desaturase 1) 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 FADS1 and FADS2 at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. [provided by RefSeq, Jul 2008]

FADS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
FADS2	XM_047427889.1 link	c.-942delT	5_prime_UTR_variant	Exon 2 of 13	XP_047283845.1
FADS2	NM_001281501.1 link	c.142-10329delT	intron_variant	Intron 1 of 11	NP_001268430.1
FADS2	NM_001281502.1 link	c.115-10329delT	intron_variant	Intron 1 of 11	NP_001268431.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
FADS2	ENST00000257261.10 link	c.142-10329delT	intron_variant	Intron 1 of 11	1	ENSP00000257261.6
FADS2	ENST00000522056.5 link	c.115-10329delT	intron_variant	Intron 1 of 11	2	ENSP00000429500.1
FADS1	ENST00000421879.5 link	c.-49+1752delA	intron_variant	Intron 1 of 4	3	ENSP00000416043.1

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43439

AN:

151888

Hom.:

8031

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0783

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.335

GnomAD4 exome

AF:

0.371

AC:

AN:

124

Hom.:

Cov.:

AF XY:

0.385

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.400

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.269

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

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:

0.286

AC:

43473

AN:

152006

Hom.:

8053

Cov.:

AF XY:

0.292

AC XY:

21676

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.0781

AC:

3244

AN:

41520

American (AMR)

AF:

0.486

AC:

7424

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

986

AN:

3470

East Asian (EAS)

AF:

0.553

AC:

2841

AN:

5134

South Asian (SAS)

AF:

0.179

AC:

863

AN:

4824

European-Finnish (FIN)

AF:

0.418

AC:

4412

AN:

10554

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.334

AC:

22675

AN:

67914

Other (OTH)

AF:

0.338

AC:

715

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1417

2834

4252

5669

7086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.180

Hom.:

411

Bravo

AF:

0.288

Asia WGS

AF:

0.370

AC:

1286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.20

Mutation Taster

=97/3

polymorphism

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over