rs3823760

Variant names:

• chr7-36541108-T-C
• rs3823760
• NM_001637.4:c.1134-617A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001637.4(AOAH):​c.1134-617A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,994 control chromosomes in the GnomAD database, including 20,633 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 0.52 (20633 hom., cov: 32)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOAH	NM_001637.4	c.1134-617A>G		intron_variant	Intron 15 of 20	ENST00000617537.5	NP_001628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOAH	ENST00000617537.5	c.1134-617A>G		intron_variant	Intron 15 of 20	1	NM_001637.4	ENSP00000483783.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78922 AN: 151874 Hom.: 20620 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.520 AC: 78987 AN: 151994 Hom.: 20633 Cov.: 32 AF XY: 0.516 AC XY: 38316 AN XY: 74288

African (AFR) AF: 0.564 AC: 23397 AN: 41450

American (AMR) AF: 0.532 AC: 8126 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2171 AN: 5148

South Asian (SAS) AF: 0.426 AC: 2057 AN: 4826

European-Finnish (FIN) AF: 0.460 AC: 4853 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35186 AN: 67950

Other (OTH) AF: 0.521 AC: 1102 AN: 2114

Alfa AF: 0.525 Hom.: 7053

Bravo AF: 0.532

Asia WGS AF: 0.471 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.54
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3823760; hg19: chr7-36580714;