Variant 19-17309480-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000593489.1(ABHD8):c.40+687C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 549,694 control chromosomes in the GnomAD database, including 183,097 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 0.84 ( 54421 hom., cov: 31)

Exomes 𝑓: 0.79 ( 128676 hom. )

Consequence

ABHD8
ENST00000593489.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Variant links:

Genes affected

ABHD8 (HGNC:23759): (abhydrolase domain containing 8) This gene is upstream of, and in a head-to-head orientation with the gene for the mitochondrial ribosomal protein L34. The predicted protein contains alpha/beta hydrolase fold and secretory lipase domains. [provided by RefSeq, Jul 2008]

ABHD8 links:

DDA1 (HGNC:28360): (DET1 and DDB1 associated 1) Involved in protein polyubiquitination. Part of Cul4-RING E3 ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

DDA1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD8	ENST00000593489.1 linkuse as main transcript	c.40+687C>A		intron_variant		4
DDA1	ENST00000593466.5 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.837

AC:

127286

AN:

151994

Hom.:

54368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.947

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.707

Gnomad ASJ

AF:

0.797

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.737

Gnomad FIN

AF:

0.911

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.834

Gnomad OTH

AF:

0.807

GnomAD4 exome

AF:

0.794

AC:

315830

AN:

397582

Hom.:

128676

Cov.:

AF XY:

0.791

AC XY:

166922

AN XY:

210932

show subpopulations

Gnomad4 AFR exome

AF:

0.947

Gnomad4 AMR exome

AF:

0.674

Gnomad4 ASJ exome

AF:

0.800

Gnomad4 EAS exome

AF:

0.372

Gnomad4 SAS exome

AF:

0.747

Gnomad4 FIN exome

AF:

0.903

Gnomad4 NFE exome

AF:

0.831

Gnomad4 OTH exome

AF:

0.801

GnomAD4 genome

AF:

0.838

AC:

127402

AN:

152112

Hom.:

54421

Cov.:

AF XY:

0.832

AC XY:

61820

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.947

Gnomad4 AMR

AF:

0.707

Gnomad4 ASJ

AF:

0.797

Gnomad4 EAS

AF:

0.391

Gnomad4 SAS

AF:

0.738

Gnomad4 FIN

AF:

0.911

Gnomad4 NFE

AF:

0.834

Gnomad4 OTH

AF:

0.810

Alfa

AF:

0.823

Hom.:

16620

Bravo

AF:

0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.36

DANN

Benign

0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over