rs2158423

Positions:

• chr8-90016131-G-A
• chr8-90016131-G-T

Variant summary

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

The NM_001359.2(DECR1):​c.70-993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,022 control chromosomes in the GnomAD database, including 6,533 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 0.22 (6533 hom., cov: 32)
• Consequence: DECR1 NM_001359.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

DECR1 (HGNC:2753): (2,4-dienoyl-CoA reductase 1) Enables 2,4-dienoyl-CoA reductase (NADPH) activity; NADPH binding activity; and identical protein binding activity. Involved in fatty acid beta-oxidation. Located in cytosol; mitochondrion; and nucleoplasm. Part of catalytic complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DECR1	NM_001359.2	c.70-993G>A		intron_variant		ENST00000220764.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DECR1	ENST00000220764.7	c.70-993G>A		intron_variant		1	NM_001359.2	P1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33136 AN: 151904 Hom.: 6489 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.219 AC: 33256 AN: 152022 Hom.: 6533 Cov.: 32 AF XY: 0.220 AC XY: 16370 AN XY: 74306

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.0763

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.208

Alfa AF: 0.0870 Hom.: 237

Bravo AF: 0.243

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.66

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: rs2158423; hg19: chr8-91028359;