11-61837342-C-A

Variant names:

• chr11-61837342-C-A
• rs174577
• NM_004265.4:c.208-436C>A

Variant summary

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

The NM_004265.4(FADS2):​c.208-436C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,998 control chromosomes in the GnomAD database, including 11,466 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 0.38 (11466 hom., cov: 32)
• Consequence: FADS2 NM_004265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 117 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=-0.88).
• 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 rank	MANE	Protein	UniProt
FADS2	NM_004265.4	c.208-436C>A		intron_variant	Intron 1 of 11	ENST00000278840.9	NP_004256.1
FADS2	NM_001281501.1	c.142-436C>A		intron_variant	Intron 1 of 11		NP_001268430.1
FADS2	NM_001281502.1	c.115-436C>A		intron_variant	Intron 1 of 11		NP_001268431.1
FADS2	XM_047427889.1	c.208-436C>A		intron_variant	Intron 2 of 12		XP_047283845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FADS2	ENST00000278840.9	c.208-436C>A		intron_variant	Intron 1 of 11	1	NM_004265.4	ENSP00000278840.4

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57173 AN: 151880 Hom.: 11432 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.377 AC: 57239 AN: 151998 Hom.: 11466 Cov.: 32 AF XY: 0.379 AC XY: 28167 AN XY: 74288

African (AFR) AF: 0.369 AC: 15278 AN: 41454

American (AMR) AF: 0.531 AC: 8111 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2858 AN: 5164

South Asian (SAS) AF: 0.182 AC: 876 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4453 AN: 10550

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23401 AN: 67958

Other (OTH) AF: 0.405 AC: 856 AN: 2112

Alfa AF: 0.359 Hom.: 39303

Bravo AF: 0.390

Asia WGS AF: 0.394 AC: 1370 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	0.90
DANN	Benign	0.35
PhyloP100		-0.029
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs174577; hg19: chr11-61604814;