rs1535

chr11-61830500-A-Gchr11-61830500-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004265.4(FADS2):c.207+1903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,126 control chromosomes in the GnomAD database, including 8,690 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 0.31 (8690 hom., cov: 32)
• Consequence: FADS2 NM_004265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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
FADS2	NM_004265.4	c.207+1903A>G		intron_variant		ENST00000278840.9
FADS2	NM_001281501.1	c.142-7278A>G		intron_variant
FADS2	NM_001281502.1	c.115-7278A>G		intron_variant
FADS2	XM_047427889.1	c.207+1903A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FADS2	ENST00000278840.9	c.207+1903A>G		intron_variant		1	NM_004265.4	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47199 AN: 152008 Hom.: 8667 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.311 AC: 47239 AN: 152126 Hom.: 8690 Cov.: 32 AF XY: 0.315 AC XY: 23456 AN XY: 74350

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.353

Alfa AF: 0.330 Hom.: 19269

Bravo AF: 0.315

Asia WGS AF: 0.380 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.7
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs1535; hg19: chr11-61597972;