rs174579

Variant names:

• chr11-61838141-C-T
• rs174579
• NM_004265.4:c.318+253C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004265.4(FADS2):​c.318+253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,138 control chromosomes in the GnomAD database, including 2,489 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 0.16 (2489 hom., cov: 32)
• Consequence: FADS2 NM_004265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 49 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FADS2	NM_004265.4	c.318+253C>T		intron_variant	Intron 2 of 11	ENST00000278840.9	NP_004256.1
FADS2	NM_001281501.1	c.252+253C>T		intron_variant	Intron 2 of 11		NP_001268430.1
FADS2	NM_001281502.1	c.225+253C>T		intron_variant	Intron 2 of 11		NP_001268431.1
FADS2	XM_047427889.1	c.318+253C>T		intron_variant	Intron 3 of 12		XP_047283845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FADS2	ENST00000278840.9	c.318+253C>T		intron_variant	Intron 2 of 11	1	NM_004265.4	ENSP00000278840.4

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24127 AN: 152020 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.159 AC: 24127 AN: 152138 Hom.: 2489 Cov.: 32 AF XY: 0.155 AC XY: 11521 AN XY: 74370

African (AFR) AF: 0.0473 AC: 1964 AN: 41530

American (AMR) AF: 0.260 AC: 3967 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.143 AC: 738 AN: 5174

South Asian (SAS) AF: 0.106 AC: 513 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14281 AN: 67982

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.195 Hom.: 2813

Bravo AF: 0.164

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.85
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs174579; hg19: chr11-61605613;