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GeneBe

rs174547

Variant summary

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

The NM_013402.7(FADS1):c.1248+52A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,472,252 control chromosomes in the GnomAD database, including 90,604 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 0.29 ( 8147 hom., cov: 32)
Exomes 𝑓: 0.34 ( 82457 hom. )

Consequence

FADS1
NM_013402.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366
Variant links:
Genes affected
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]
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]

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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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FADS1NM_013402.7 linkuse as main transcriptc.1248+52A>G intron_variant ENST00000350997.12
FADS1XM_011545022.3 linkuse as main transcriptc.1035+52A>G intron_variant
FADS1XM_047426935.1 linkuse as main transcriptc.825+52A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FADS1ENST00000350997.12 linkuse as main transcriptc.1248+52A>G intron_variant 1 NM_013402.7 P1

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43701
AN:
151986
Hom.:
8125
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0782
Gnomad AMI
AF:
0.233
Gnomad AMR
AF:
0.487
Gnomad ASJ
AF:
0.286
Gnomad EAS
AF:
0.554
Gnomad SAS
AF:
0.178
Gnomad FIN
AF:
0.421
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.336
Gnomad OTH
AF:
0.336
GnomAD4 exome
AF:
0.338
AC:
446677
AN:
1320148
Hom.:
82457
Cov.:
20
AF XY:
0.332
AC XY:
220249
AN XY:
664042
show subpopulations
Gnomad4 AFR exome
AF:
0.0617
Gnomad4 AMR exome
AF:
0.650
Gnomad4 ASJ exome
AF:
0.279
Gnomad4 EAS exome
AF:
0.457
Gnomad4 SAS exome
AF:
0.170
Gnomad4 FIN exome
AF:
0.424
Gnomad4 NFE exome
AF:
0.339
Gnomad4 OTH exome
AF:
0.345
GnomAD4 genome
AF:
0.288
AC:
43735
AN:
152104
Hom.:
8147
Cov.:
32
AF XY:
0.293
AC XY:
21819
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0780
Gnomad4 AMR
AF:
0.488
Gnomad4 ASJ
AF:
0.286
Gnomad4 EAS
AF:
0.554
Gnomad4 SAS
AF:
0.180
Gnomad4 FIN
AF:
0.421
Gnomad4 NFE
AF:
0.336
Gnomad4 OTH
AF:
0.339
Alfa
AF:
0.327
Hom.:
16839
Bravo
AF:
0.288
Asia WGS
AF:
0.375
AC:
1302
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
7.1
Dann
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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.

Other links and lift over

dbSNP: rs174547; hg19: chr11-61570783; COSMIC: COSV63520556; COSMIC: COSV63520556; API