NM_013402.7:c.*2130G>T

Variant names:

• chr11-61800281-C-A
• rs174544
• NM_013402.7:c.*2130G>T

Variant summary

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

The NM_013402.7(FADS1):​c.*2130G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,650 control chromosomes in the GnomAD database, including 6,802 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 0.26 (6795 hom., cov: 31)
  • Exomes 𝑓: 0.28 (7 hom.)
• Consequence: FADS1 NM_013402.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 66 publications found

Genes affected

FADS1 (HGNC:3574): (fatty acid desaturase 1) 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]

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013402.7. 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
	FADS1	NM_013402.7	MANE Select	c.*2130G>T		3_prime_UTR	Exon 12 of 12	NP_037534.5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FADS1	ENST00000350997.12	TSL:1 MANE Select	c.*2130G>T		3_prime_UTR	Exon 12 of 12	ENSP00000322229.9	A0A0A0MR51
	FADS1	ENST00000935427.1		c.*2130G>T		3_prime_UTR	Exon 12 of 12	ENSP00000605486.1
	FADS1	ENST00000935426.1		c.*2130G>T		3_prime_UTR	Exon 11 of 11	ENSP00000605485.1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39360 AN: 151352 Hom.: 6775 Cov.: 31

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.278 AC: 50 AN: 180 Hom.: 7 Cov.: 0 AF XY: 0.313 AC XY: 35 AN XY: 112

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

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.261 AC: 36 AN: 138

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: 0.353 AC: 12 AN: 34

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.260 AC: 39394 AN: 151470 Hom.: 6795 Cov.: 31 AF XY: 0.267 AC XY: 19747 AN XY: 73990

African (AFR) AF: 0.0710 AC: 2932 AN: 41322

American (AMR) AF: 0.461 AC: 7016 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 760 AN: 3462

East Asian (EAS) AF: 0.539 AC: 2764 AN: 5126

South Asian (SAS) AF: 0.163 AC: 784 AN: 4798

European-Finnish (FIN) AF: 0.395 AC: 4120 AN: 10422

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20092 AN: 67818

Other (OTH) AF: 0.304 AC: 641 AN: 2106

Alfa AF: 0.567 Hom.: 7220

Bravo AF: 0.263

Asia WGS AF: 0.356 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-0.23
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: rs174544; hg19: chr11-61567753;