Variant rs10156191 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001091.4(AOC1):c.47C>T(p.Thr16Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,613,618 control chromosomes in the GnomAD database, including 62,508 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.33 ( 9422 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53086 hom. )

Consequence

AOC1
NM_001091.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132

Variant links:

Genes affected

AOC1 (HGNC:80): (amine oxidase copper containing 1) This gene encodes a metal-binding membrane glycoprotein that oxidatively deaminates putrescine, histamine, and related compounds. The encoded protein is inhibited by amiloride, a diuretic that acts by closing epithelial sodium ion channels. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]

AOC1 links:

LOC105375567 (HGNC:):

LOC105375567 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.31944E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOC1	NM_001091.4 linkuse as main transcript	c.47C>T	p.Thr16Met	missense_variant	2/5	ENST00000360937.9	NP_001082.2
LOC105375567	XR_928171.3 linkuse as main transcript	n.123-15072G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9 linkuse as main transcript	c.47C>T	p.Thr16Met	missense_variant	2/5	1	NM_001091.4	ENSP00000354193	P2	P19801-1

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49511

AN:

151884

Hom.:

9397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.261

AC:

64895

AN:

248794

Hom.:

9561

AF XY:

0.260

AC XY:

35099

AN XY:

135108

show subpopulations

Gnomad AFR exome

AF:

0.532

Gnomad AMR exome

AF:

0.173

Gnomad ASJ exome

AF:

0.282

Gnomad EAS exome

AF:

0.133

Gnomad SAS exome

AF:

0.264

Gnomad FIN exome

AF:

0.287

Gnomad NFE exome

AF:

0.264

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.262

AC:

382663

AN:

1461616

Hom.:

53086

Cov.:

AF XY:

0.261

AC XY:

189675

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.524

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.281

Gnomad4 EAS exome

AF:

0.114

Gnomad4 SAS exome

AF:

0.262

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.262

GnomAD4 genome

AF:

0.326

AC:

49577

AN:

152002

Hom.:

9422

Cov.:

AF XY:

0.323

AC XY:

24038

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.520

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.123

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.282

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.265

Hom.:

12444

Bravo

AF:

0.331

TwinsUK

AF:

0.257

AC:

953

ALSPAC

AF:

0.250

AC:

962

ESP6500AA

AF:

0.508

AC:

1966

ESP6500EA

AF:

0.267

AC:

2203

ExAC

AF:

0.270

AC:

32562

Asia WGS

AF:

0.215

AC:

752

AN:

3478

EpiCase

AF:

0.265

EpiControl

AF:

0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.70

CADD

Benign

2.5

DANN

Benign

0.63

DEOGEN2

Benign

0.086

T;T;.;T;.;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0017

LIST_S2

Benign

0.23

.;T;T;.;T;T

MetaRNN

Benign

0.000033

T;T;T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

-0.84

N;N;.;N;N;.

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

0.36

N;N;N;N;N;N

REVEL

Benign

0.024

Sift

Benign

0.21

T;T;T;T;T;T

Sift4G

Benign

0.18

T;T;T;T;T;T

Polyphen

0.0010

B;B;.;B;.;.

Vest4

0.030

MPC

0.22

ClinPred

0.0019

GERP RS

-0.64

Varity_R

0.013

gMVP

0.22

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over