rs1000778

Variant names:

• chr11-61887833-A-G
• rs1000778
• NM_021727.5:c.213+3336T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-61887833-A-G
• chr11-61887833-A-T

Variant summary

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

The NM_021727.5(FADS3):​c.213+3336T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,124 control chromosomes in the GnomAD database, including 30,179 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 0.60 (30179 hom., cov: 33)
• Consequence: FADS3 NM_021727.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 66 publications found

Genes affected

FADS3 (HGNC:3576): (fatty acid desaturase 3) 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 FADS1 and FADS2 at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. [provided by RefSeq, Jul 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021727.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS3	NM_021727.5	MANE Select	c.213+3336T>C		intron	N/A	NP_068373.1	Q9Y5Q0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS3	ENST00000278829.7	TSL:1 MANE Select	c.213+3336T>C		intron	N/A	ENSP00000278829.2	Q9Y5Q0
	FADS3	ENST00000969795.1		c.213+3336T>C		intron	N/A	ENSP00000639854.1
	FADS3	ENST00000969794.1		c.213+3336T>C		intron	N/A	ENSP00000639853.1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90845 AN: 152006 Hom.: 30181 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.597 AC: 90839 AN: 152124 Hom.: 30179 Cov.: 33 AF XY: 0.599 AC XY: 44509 AN XY: 74348

African (AFR) AF: 0.302 AC: 12544 AN: 41484

American (AMR) AF: 0.517 AC: 7908 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2633 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3571 AN: 5172

South Asian (SAS) AF: 0.632 AC: 3046 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8196 AN: 10580

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50729 AN: 67994

Other (OTH) AF: 0.612 AC: 1294 AN: 2116

Alfa AF: 0.690 Hom.: 156627

Bravo AF: 0.563

Asia WGS AF: 0.611 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.17
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: rs1000778; hg19: chr11-61655305;