Variant rs174547 details in Genebe, Genetics Data Aggregator

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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366

Links

FADS1 (HGNC:3574):

FADS2 (HGNC:3575):

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	Effect	MANE
FADS1	NM_013402.7 linkuse as main transcript	c.1248+52A>G	intron_variant	ENST00000350997.12
FADS1	XM_011545022.3 linkuse as main transcript	c.1035+52A>G	intron_variant
FADS1	XM_047426935.1 linkuse as main transcript	c.825+52A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FADS1	ENST00000350997.12 linkuse as main transcript	c.1248+52A>G		intron_variant		1	NM_013402.7	P1

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43701

AN:

151986

Hom.:

8125

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over