rs2015599

Positions:

• chr12-29282547-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	UniProt
FAR2	NM_001271783.2	c.190-10753G>A		intron_variant		ENST00000536681.8
LOC100506606	NR_103860.1	n.1059-187C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAR2	ENST00000536681.8	c.190-10753G>A		intron_variant		1	NM_001271783.2	P1
	ENST00000553105.1	n.1059-187C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.472

Alfa AF: 0.459 Hom.: 15985

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

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: rs2015599; hg19: chr12-29435480;