rs1793426

Variant names:

• chr11-56916274-G-A
• rs1793426
• ENST00000611807.1:n.895G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000611807.1(FADS2B):​n.895G>A 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 0.308 in 151,908 control chromosomes in the GnomAD database, including 7,434 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 (7434 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: FADS2B ENST00000611807.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

FADS2B (HGNC:43618): (fatty acid desaturase 2B (pseudogene)) Predicted to enable oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water. Predicted to be involved in lipid metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105369310 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369310	XR_950121.2	n.2570-5787C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FADS2B	ENST00000611807.1	n.895G>A		non_coding_transcript_exon_variant	Exon 6 of 12	6

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46812 AN: 151778 Hom.: 7437 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.308 AC: 46801 AN: 151896 Hom.: 7434 Cov.: 32 AF XY: 0.307 AC XY: 22811 AN XY: 74212

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.278

Alfa AF: 0.325 Hom.: 12095

Bravo AF: 0.296

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1793426; hg19: chr11-56683750;