rs174541

chr11-61798436-T-C

Variant summary

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

The ENST00000689245.1(ENSG00000289268):n.710A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,164 control chromosomes in the GnomAD database, including 8,709 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 0.30 (8709 hom., cov: 31)
• Consequence: ENST00000689245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

(HGNC:):

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 = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689245.1	n.710A>G		non_coding_transcript_exon_variant	1/1
FADS2	ENST00000574708.5	n.49+5408T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45224 AN: 152044 Hom.: 8687 Cov.: 31

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.297 AC: 45257 AN: 152164 Hom.: 8709 Cov.: 31 AF XY: 0.304 AC XY: 22625 AN XY: 74402

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.345

Alfa AF: 0.315 Hom.: 1090

Bravo AF: 0.297

Asia WGS AF: 0.378 AC: 1313 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	1.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174541; hg19: chr11-61565908;