rs4723563

Positions:

• chr7-36717858-C-T

Variant summary

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

The NM_001637.4(AOAH):​c.127+6164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,310 control chromosomes in the GnomAD database, including 44,275 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 0.76 (44275 hom., cov: 27)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOAH	NM_001637.4	c.127+6164G>A		intron_variant		ENST00000617537.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOAH	ENST00000617537.5	c.127+6164G>A		intron_variant		1	NM_001637.4	P1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115535 AN: 151192 Hom.: 44229 Cov.: 27

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.764 AC: 115640 AN: 151310 Hom.: 44275 Cov.: 27 AF XY: 0.770 AC XY: 56926 AN XY: 73900

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.770

Alfa AF: 0.758 Hom.: 88354

Bravo AF: 0.766

Asia WGS AF: 0.859 AC: 2982 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.63

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: rs4723563; hg19: chr7-36757463;