rs2015599

Variant names:

• chr12-29282547-G-A
• rs2015599
• NM_001271783.2:c.190-10753G>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.190-10753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,920 control chromosomes in the GnomAD database, including 20,017 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 0.50 (20017 hom., cov: 32)
• Consequence: FAR2 NM_001271783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 22 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]

ENSG00000257176 (HGNC:58443):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAR2	NM_001271783.2	c.190-10753G>A		intron_variant	Intron 2 of 11	ENST00000536681.8	NP_001258712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAR2	ENST00000536681.8	c.190-10753G>A		intron_variant	Intron 2 of 11	1	NM_001271783.2	ENSP00000443291.2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76338 AN: 151802 Hom.: 19986 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.503 AC: 76432 AN: 151920 Hom.: 20017 Cov.: 32 AF XY: 0.498 AC XY: 36964 AN XY: 74232

African (AFR) AF: 0.659 AC: 27309 AN: 41444

American (AMR) AF: 0.365 AC: 5566 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1507 AN: 3464

East Asian (EAS) AF: 0.509 AC: 2629 AN: 5166

South Asian (SAS) AF: 0.499 AC: 2401 AN: 4816

European-Finnish (FIN) AF: 0.453 AC: 4768 AN: 10534

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30848 AN: 67936

Other (OTH) AF: 0.472 AC: 995 AN: 2106

Alfa AF: 0.468 Hom.: 51407

Bravo AF: 0.498

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.30
PhyloP100		-3.0
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: rs2015599; hg19: chr12-29435480;