NM_001271783.2:c.-39+53384C>A

Variant names:

• chr12-29202791-C-A
• rs958478
• NM_001271783.2:c.-39+53384C>A

Variant summary

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

The NM_001271783.2(FAR2):​c.-39+53384C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,044 control chromosomes in the GnomAD database, including 43,445 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 0.74 (43445 hom., cov: 32)
• Consequence: FAR2 NM_001271783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 publications found

Genes affected

FAR2 (HGNC:25531): (fatty acyl-CoA reductase 2) This gene belongs to the short chain dehydrogenase/reductase superfamily. It encodes a reductase enzyme involved in the first step of wax biosynthesis wherein fatty acids are converted to fatty alcohols. The encoded peroxisomal protein utilizes saturated fatty acids of 16 or 18 carbons as preferred substrates. Alternatively spliced transcript variants have been observed for this gene. Related pseudogenes have been identified on chromosomes 2, 14 and 22. [provided by RefSeq, Nov 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271783.2. 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
	FAR2	NM_001271783.2	MANE Select	c.-39+53384C>A		intron	N/A	NP_001258712.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAR2	ENST00000536681.8	TSL:1 MANE Select	c.-39+53384C>A		intron	N/A	ENSP00000443291.2
	FAR2	ENST00000686419.1		c.-39+53384C>A		intron	N/A	ENSP00000509644.1
	FAR2	ENST00000547759.2	TSL:5	c.-39+53384C>A		intron	N/A	ENSP00000447467.2

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112053 AN: 151926 Hom.: 43420 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.737 AC: 112125 AN: 152044 Hom.: 43445 Cov.: 32 AF XY: 0.737 AC XY: 54814 AN XY: 74330

African (AFR) AF: 0.481 AC: 19942 AN: 41444

American (AMR) AF: 0.817 AC: 12486 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4677 AN: 5160

South Asian (SAS) AF: 0.695 AC: 3344 AN: 4814

European-Finnish (FIN) AF: 0.843 AC: 8916 AN: 10578

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57720 AN: 67998

Other (OTH) AF: 0.721 AC: 1515 AN: 2102

Alfa AF: 0.784 Hom.: 5995

Bravo AF: 0.729

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-0.93
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: rs958478; hg19: chr12-29355724;