chr7-36577011-T-C

Variant names:

• chr7-36577011-T-C
• rs2727831
• NM_001637.4:c.939-355A>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.939-355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 150,622 control chromosomes in the GnomAD database, including 28,085 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 0.61 (28085 hom., cov: 28)
• Consequence: AOAH NM_001637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AOAH	NM_001637.4	c.939-355A>G		intron_variant	Intron 12 of 20	ENST00000617537.5	NP_001628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AOAH	ENST00000617537.5	c.939-355A>G		intron_variant	Intron 12 of 20	1	NM_001637.4	ENSP00000483783.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91140 AN: 150532 Hom.: 28055 Cov.: 28

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.606 AC: 91214 AN: 150622 Hom.: 28085 Cov.: 28 AF XY: 0.602 AC XY: 44247 AN XY: 73506

African (AFR) AF: 0.711 AC: 29075 AN: 40902

American (AMR) AF: 0.628 AC: 9520 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1911 AN: 3462

East Asian (EAS) AF: 0.469 AC: 2407 AN: 5130

South Asian (SAS) AF: 0.541 AC: 2595 AN: 4794

European-Finnish (FIN) AF: 0.526 AC: 5319 AN: 10108

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38598 AN: 67786

Other (OTH) AF: 0.620 AC: 1295 AN: 2088

Alfa AF: 0.590 Hom.: 3355

Bravo AF: 0.626

Asia WGS AF: 0.548 AC: 1906 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-1.5
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: rs2727831; hg19: chr7-36616617;