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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 0.288 in 151986 control chromosomes in the gnomAD Genomes database, including 8125 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 ( 8125 hom., cov: 32)

Consequence

FADS1
NM_013402.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366

Links

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
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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
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
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
5.5
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;