rs2072113

Variant names:

• chr11-61837495-C-T
• rs2072113
• NM_004265.4:c.208-283C>T

Variant summary

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

The NM_004265.4(FADS2):​c.208-283C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,168 control chromosomes in the GnomAD database, including 2,304 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 0.15 (2304 hom., cov: 32)
• Consequence: FADS2 NM_004265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 21 publications found

Genes affected

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004265.4. 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
	FADS2	NM_004265.4	MANE Select	c.208-283C>T		intron	N/A	NP_004256.1
	FADS2	NM_001281501.1		c.142-283C>T		intron	N/A	NP_001268430.1
	FADS2	NM_001281502.1		c.115-283C>T		intron	N/A	NP_001268431.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS2	ENST00000278840.9	TSL:1 MANE Select	c.208-283C>T		intron	N/A	ENSP00000278840.4
	FADS2	ENST00000257261.10	TSL:1	c.142-283C>T		intron	N/A	ENSP00000257261.6
	FADS2	ENST00000521849.5	TSL:1	c.208-283C>T		intron	N/A	ENSP00000431091.1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23508 AN: 152050 Hom.: 2293 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.155 AC: 23561 AN: 152168 Hom.: 2304 Cov.: 32 AF XY: 0.163 AC XY: 12128 AN XY: 74384

African (AFR) AF: 0.128 AC: 5321 AN: 41522

American (AMR) AF: 0.234 AC: 3577 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2121 AN: 5168

South Asian (SAS) AF: 0.0747 AC: 361 AN: 4830

European-Finnish (FIN) AF: 0.283 AC: 2989 AN: 10568

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8421 AN: 68012

Other (OTH) AF: 0.160 AC: 337 AN: 2110

Alfa AF: 0.146 Hom.: 414

Bravo AF: 0.154

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.043
DANN	Benign	0.63
PhyloP100		-3.1
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: rs2072113; hg19: chr11-61604967;