rs1561131

chr12-29154998-G-Achr12-29154998-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271783.2(FAR2):c.-39+5591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,098 control chromosomes in the GnomAD database, including 33,308 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 0.65 (33308 hom., cov: 32)
• Consequence: FAR2 NM_001271783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAR2	NM_001271783.2	c.-39+5591G>A		intron_variant		ENST00000536681.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAR2	ENST00000536681.8	c.-39+5591G>A		intron_variant		1	NM_001271783.2	P1
	ENST00000662829.1	n.253+2535C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98181 AN: 151978 Hom.: 33294 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.646 AC: 98225 AN: 152098 Hom.: 33308 Cov.: 32 AF XY: 0.644 AC XY: 47865 AN XY: 74346

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.614

Alfa AF: 0.691 Hom.: 4635

Bravo AF: 0.644

Asia WGS AF: 0.633 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.8
Dann	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561131; hg19: chr12-29307931;