rs6968002

chr7-36525098-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.1523-2983G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,178 control chromosomes in the GnomAD database, including 695 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 0.075 (695 hom., cov: 32)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOAH	NM_001637.4	c.1523-2983G>A		intron_variant		ENST00000617537.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOAH	ENST00000617537.5	c.1523-2983G>A		intron_variant		1	NM_001637.4	P1
AOAH	ENST00000617267.4	c.1523-2983G>A		intron_variant		1
AOAH	ENST00000612871.4	c.1427-2983G>A		intron_variant		2
AOAH	ENST00000614254.1	n.268-2983G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11436 AN: 152060 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0752 AC: 11440 AN: 152178 Hom.: 695 Cov.: 32 AF XY: 0.0720 AC XY: 5361 AN XY: 74422

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0541 Hom.: 119

Bravo AF: 0.0799

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.84
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6968002; hg19: chr7-36564704;