rs1805880

Positions:

• chr8-90019960-T-G

Variant summary

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

The NM_001359.2(DECR1):​c.417+788T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,304 control chromosomes in the GnomAD database, including 284 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 0.043 (284 hom., cov: 32)
• Consequence: DECR1 NM_001359.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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]

DECR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DECR1	NM_001359.2	c.417+788T>G		intron_variant		ENST00000220764.7	NP_001350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DECR1	ENST00000220764.7	c.417+788T>G		intron_variant		1	NM_001359.2	ENSP00000220764.2

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6517 AN: 152184 Hom.: 283 Cov.: 32

Gnomad AFR AF: 0.00950

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0428 AC: 6525 AN: 152304 Hom.: 284 Cov.: 32 AF XY: 0.0480 AC XY: 3575 AN XY: 74480

Gnomad4 AFR AF: 0.00947

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0784

Gnomad4 NFE AF: 0.0304

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0383 Hom.: 20

Bravo AF: 0.0466

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.81

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: rs1805880; hg19: chr8-91032188;