12-29233329-G-A

Variant names:

• chr12-29233329-G-A
• rs12310555
• NM_001271783.2:c.-38-37083G>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.-38-37083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,022 control chromosomes in the GnomAD database, including 3,182 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 0.18 (3182 hom., cov: 32)
• Consequence: FAR2 NM_001271783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• 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]

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 = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAR2	NM_001271783.2	c.-38-37083G>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.-38-37083G>A		intron_variant	Intron 1 of 11	1	NM_001271783.2	ENSP00000443291.2

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26768 AN: 151904 Hom.: 3179 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.176 AC: 26798 AN: 152022 Hom.: 3182 Cov.: 32 AF XY: 0.179 AC XY: 13298 AN XY: 74320

African (AFR) AF: 0.333 AC: 13799 AN: 41440

American (AMR) AF: 0.0989 AC: 1509 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5156

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4812

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10588

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6965 AN: 67980

Other (OTH) AF: 0.152 AC: 321 AN: 2110

Alfa AF: 0.148 Hom.: 358

Bravo AF: 0.177

Asia WGS AF: 0.240 AC: 835 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	1.5
DANN	Benign	0.39
PhyloP100		-0.25
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: rs12310555; hg19: chr12-29386262;