rs4931170

Positions:

• chr12-29235839-A-G

Variant summary

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

The ENST00000536681.8(FAR2):​c.-38-34573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,076 control chromosomes in the GnomAD database, including 8,879 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 0.30 (8879 hom., cov: 32)
• Consequence: FAR2 ENST00000536681.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAR2	NM_001271783.2	c.-38-34573A>G		intron_variant		ENST00000536681.8	NP_001258712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAR2	ENST00000536681.8	c.-38-34573A>G		intron_variant		1	NM_001271783.2	ENSP00000443291	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46160 AN: 151958 Hom.: 8873 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.304 AC: 46165 AN: 152076 Hom.: 8879 Cov.: 32 AF XY: 0.310 AC XY: 23008 AN XY: 74314

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.308

Alfa AF: 0.371 Hom.: 15212

Bravo AF: 0.299

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.78

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: rs4931170; hg19: chr12-29388772;