rs60023210

Positions:

• chr7-36648149-G-A

Variant summary

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

The NM_001637.4(AOAH):​c.391-10239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,726 control chromosomes in the GnomAD database, including 9,139 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 0.34 (9139 hom., cov: 31)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOAH	NM_001637.4	c.391-10239C>T		intron_variant		ENST00000617537.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOAH	ENST00000617537.5	c.391-10239C>T		intron_variant		1	NM_001637.4	P1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51380 AN: 151610 Hom.: 9134 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.339 AC: 51413 AN: 151726 Hom.: 9139 Cov.: 31 AF XY: 0.327 AC XY: 24232 AN XY: 74120

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.325

Alfa AF: 0.350 Hom.: 1222

Bravo AF: 0.341

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.20

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: rs60023210; hg19: chr7-36687754;