chr11-56916274-G-A

Position:

• chr11-56916274-G-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:):

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/exons	MANE	Protein	UniProt
LOC105369310	XR_950121.2	n.2570-5787C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FADS2B	ENST00000611807.1	n.895G>A		non_coding_transcript_exon_variant	6/12	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;