dbSNP rs66698963: FADS2:c.208-2735_208-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG (chr11-61835024-CCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGGACTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004265.4(FADS2):c.208-2735_208-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000094 ( 0 hom., cov: 0)

Consequence

FADS2
NM_004265.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Publications

14 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
FADS2	NM_004265.4 link	c.208-2735_208-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG	intron_variant	Intron 1 of 11	ENST00000278840.9	NP_004256.1
FADS2	NM_001281501.1 link	c.142-2735_142-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG	intron_variant	Intron 1 of 11		NP_001268430.1
FADS2	NM_001281502.1 link	c.115-2735_115-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG	intron_variant	Intron 1 of 11		NP_001268431.1
FADS2	XM_047427889.1 link	c.208-2735_208-2692delACTTCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGG	intron_variant	Intron 2 of 12		XP_047283845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FADS2	ENST00000278840.9 link	c.208-2753_208-2710delCTCCCTGCCTCCCCAGGGACTTCTCCCTGCCTCCCCAGGGACTT		intron_variant	Intron 1 of 11	1	NM_004265.4	ENSP00000278840.4

Frequencies

GnomAD3 genomes

AF:

0.0000943

AC:

AN:

137868

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000270

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000373

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000110

Gnomad OTH

AF:

0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0000943

AC:

AN:

137868

Hom.:

Cov.:

AF XY:

0.0000603

AC XY:

AN XY:

66316

show subpopulations

African (AFR)

AF:

0.0000270

AC:

AN:

37086

American (AMR)

AF:

0.000373

AC:

AN:

13416

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3328

East Asian (EAS)

AF:

0.00

AC:

AN:

4564

South Asian (SAS)

AF:

0.00

AC:

AN:

4382

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8450

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.000110

AC:

AN:

63676

Other (OTH)

AF:

0.00

AC:

AN:

1838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00

Hom.:

898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over