8-90010890-T-C

Position:

• chr8-90010890-T-C

Variant summary

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

The NM_001359.2(DECR1):​c.70-6234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,060 control chromosomes in the GnomAD database, including 21,993 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 0.51 (21993 hom., cov: 32)
• Consequence: DECR1 NM_001359.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DECR1	NM_001359.2	c.70-6234T>C		intron_variant		ENST00000220764.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DECR1	ENST00000220764.7	c.70-6234T>C		intron_variant		1	NM_001359.2	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77168 AN: 151942 Hom.: 21923 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.508 AC: 77310 AN: 152060 Hom.: 21993 Cov.: 32 AF XY: 0.514 AC XY: 38209 AN XY: 74298

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.493

Alfa AF: 0.455 Hom.: 2193

Bravo AF: 0.525

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.022
DANN	Benign	0.26

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: rs1805809; hg19: chr8-91023118;