chr11-61830500-A-G

Variant names:

• chr11-61830500-A-G
• rs1535
• NM_004265.4:c.207+1903A>G

Variant summary

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

The NM_004265.4(FADS2):​c.207+1903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,126 control chromosomes in the GnomAD database, including 8,690 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 (8690 hom., cov: 32)
• Consequence: FADS2 NM_004265.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685
• Publications: 257 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS2	NM_004265.4	MANE Select	c.207+1903A>G		intron	N/A	NP_004256.1
	FADS2	NM_001281501.1		c.142-7278A>G		intron	N/A	NP_001268430.1
	FADS2	NM_001281502.1		c.115-7278A>G		intron	N/A	NP_001268431.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS2	ENST00000278840.9	TSL:1 MANE Select	c.207+1903A>G		intron	N/A	ENSP00000278840.4
	FADS2	ENST00000257261.10	TSL:1	c.142-7278A>G		intron	N/A	ENSP00000257261.6
	FADS2	ENST00000521849.5	TSL:1	c.207+1903A>G		intron	N/A	ENSP00000431091.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47199 AN: 152008 Hom.: 8667 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.311 AC: 47239 AN: 152126 Hom.: 8690 Cov.: 32 AF XY: 0.315 AC XY: 23456 AN XY: 74350

African (AFR) AF: 0.153 AC: 6335 AN: 41522

American (AMR) AF: 0.501 AC: 7658 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 986 AN: 3460

East Asian (EAS) AF: 0.553 AC: 2868 AN: 5182

South Asian (SAS) AF: 0.182 AC: 876 AN: 4822

European-Finnish (FIN) AF: 0.420 AC: 4436 AN: 10558

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23018 AN: 67986

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.331 Hom.: 40623

Bravo AF: 0.315

Asia WGS AF: 0.380 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		-0.69
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: rs1535; hg19: chr11-61597972;