rs4504543

Positions:

• chr7-36643290-T-C

Variant summary

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

The NM_001637.4(AOAH):​c.391-5380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,064 control chromosomes in the GnomAD database, including 13,193 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 0.40 (13193 hom., cov: 32)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

Genes affected

AOAH (HGNC:548): (acyloxyacyl hydrolase) This locus encodes both the light and heavy subunits of acyloxyacyl hydrolase. The encoded enzyme catalyzes the hydrolysis of acyloxylacyl-linked fatty acyl chains from bacterial lipopolysaccharides, effectively detoxifying these molecules. The encoded protein may play a role in modulating host inflammatory response to gram-negative bacteria. Alternatively spliced transcript variants have been described.[provided by RefSeq, Apr 2010]

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 = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOAH	NM_001637.4	c.391-5380A>G		intron_variant		ENST00000617537.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOAH	ENST00000617537.5	c.391-5380A>G		intron_variant		1	NM_001637.4	P1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60863 AN: 151946 Hom.: 13166 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.401 AC: 60944 AN: 152064 Hom.: 13193 Cov.: 32 AF XY: 0.390 AC XY: 28963 AN XY: 74316

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.376

Alfa AF: 0.361 Hom.: 20479

Bravo AF: 0.409

Asia WGS AF: 0.226 AC: 786 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	0.30
DANN	Benign	0.72

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: rs4504543; hg19: chr7-36682895;