ENST00000611807.2:n.895G>A

Variant names:

• chr11-56916274-G-A
• rs1793426
• ENST00000611807.2:n.895G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000611807.2(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 ENST00000611807.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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	ENST00000611807.2	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.271 AC: 11230 AN: 41444

American (AMR) AF: 0.265 AC: 4046 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3466

East Asian (EAS) AF: 0.148 AC: 761 AN: 5158

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4234 AN: 10522

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23073 AN: 67916

Other (OTH) AF: 0.278 AC: 586 AN: 2106

Alfa AF: 0.323 Hom.: 16360

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1793426; hg19: chr11-56683750;