rs6948404

Variant names:

• chr7-36570887-T-C
• rs6948404
• NM_001637.4:c.1021+5687A>G

Variant summary

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

The NM_001177506.2(AOAH):​c.1021+5687A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,280 control chromosomes in the GnomAD database, including 723 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 0.089 (723 hom., cov: 32)
• Consequence: AOAH NM_001177506.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001177506.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOAH	NM_001637.4	MANE Select	c.1021+5687A>G		intron	N/A	NP_001628.1
	AOAH	NM_001177506.2		c.1021+5687A>G		intron	N/A	NP_001170977.1
	AOAH	NM_001177507.2		c.925+5687A>G		intron	N/A	NP_001170978.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOAH	ENST00000617537.5	TSL:1 MANE Select	c.1021+5687A>G		intron	N/A	ENSP00000483783.1
	AOAH	ENST00000617267.5	TSL:1	c.1021+5687A>G		intron	N/A	ENSP00000479664.1
	AOAH	ENST00000941760.1		c.1018+5687A>G		intron	N/A	ENSP00000611819.1

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13563 AN: 152162 Hom.: 724 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0587

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0891 AC: 13568 AN: 152280 Hom.: 723 Cov.: 32 AF XY: 0.0899 AC XY: 6697 AN XY: 74462

African (AFR) AF: 0.0835 AC: 3471 AN: 41558

American (AMR) AF: 0.144 AC: 2200 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 323 AN: 3472

East Asian (EAS) AF: 0.0581 AC: 301 AN: 5184

South Asian (SAS) AF: 0.130 AC: 625 AN: 4818

European-Finnish (FIN) AF: 0.0809 AC: 859 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5491 AN: 68020

Other (OTH) AF: 0.112 AC: 236 AN: 2110

Alfa AF: 0.0856 Hom.: 2245

Bravo AF: 0.0943

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.37
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: rs6948404; hg19: chr7-36610493;