rs4931170

Variant names:

• chr12-29235839-A-G
• rs4931170
• NM_001271783.2:c.-38-34573A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018099.5(FAR2):​c.-39+11945A>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 NM_018099.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018099.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAR2	NM_001271783.2	MANE Select	c.-38-34573A>G		intron	N/A	NP_001258712.1
	FAR2	NM_018099.5		c.-39+11945A>G		intron	N/A	NP_060569.3
	FAR2	NM_001271784.2		c.-103+11945A>G		intron	N/A	NP_001258713.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAR2	ENST00000536681.8	TSL:1 MANE Select	c.-38-34573A>G		intron	N/A	ENSP00000443291.2
	FAR2	ENST00000182377.8	TSL:1	c.-39+11945A>G		intron	N/A	ENSP00000182377.4
	FAR2	ENST00000946761.1		c.-38-34573A>G		intron	N/A	ENSP00000616820.1

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

African (AFR) AF: 0.0717 AC: 2979 AN: 41554

American (AMR) AF: 0.462 AC: 7049 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3466

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5170

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4452 AN: 10556

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26417 AN: 67952

Other (OTH) AF: 0.308 AC: 648 AN: 2102

Alfa AF: 0.356 Hom.: 24488

Bravo AF: 0.299

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.089
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: rs4931170; hg19: chr12-29388772;