rs1561131

Variant names:

• chr12-29154998-G-A
• rs1561131
• NM_001271783.2:c.-39+5591G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-29154998-G-A
• chr12-29154998-G-T

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+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
• Publications: 2 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]

ENSG00000257258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAR2	NM_001271783.2	c.-39+5591G>A		intron_variant	Intron 1 of 11	ENST00000536681.8	NP_001258712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAR2	ENST00000536681.8	c.-39+5591G>A		intron_variant	Intron 1 of 11	1	NM_001271783.2	ENSP00000443291.2

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

African (AFR) AF: 0.424 AC: 17587 AN: 41458

American (AMR) AF: 0.744 AC: 11379 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2188 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3877 AN: 5164

South Asian (SAS) AF: 0.613 AC: 2951 AN: 4816

European-Finnish (FIN) AF: 0.691 AC: 7318 AN: 10584

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50704 AN: 67990

Other (OTH) AF: 0.614 AC: 1299 AN: 2116

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
PhyloP100		0.56
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: rs1561131; hg19: chr12-29307931;