rs60023210

Variant names:

• chr7-36648149-G-A
• rs60023210
• NM_001637.4:c.391-10239C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001637.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOAH	NM_001637.4	MANE Select	c.391-10239C>T		intron	N/A	NP_001628.1
	AOAH	NM_001177506.2		c.391-10239C>T		intron	N/A	NP_001170977.1
	AOAH	NM_001177507.2		c.295-10239C>T		intron	N/A	NP_001170978.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AOAH	ENST00000617537.5	TSL:1 MANE Select	c.391-10239C>T		intron	N/A	ENSP00000483783.1
	AOAH	ENST00000617267.5	TSL:1	c.391-10239C>T		intron	N/A	ENSP00000479664.1
	AOAH	ENST00000612871.4	TSL:2	c.295-10239C>T		intron	N/A	ENSP00000484305.1

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

African (AFR) AF: 0.387 AC: 15980 AN: 41328

American (AMR) AF: 0.263 AC: 4007 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1097 AN: 3468

East Asian (EAS) AF: 0.0728 AC: 376 AN: 5164

South Asian (SAS) AF: 0.142 AC: 684 AN: 4810

European-Finnish (FIN) AF: 0.293 AC: 3082 AN: 10526

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24896 AN: 67870

Other (OTH) AF: 0.325 AC: 684 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.20
PhyloP100		-0.58
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: rs60023210; hg19: chr7-36687754;