Variant 7-150857465-C-T 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.995C>T(p.Ser332Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0708 in 1,612,628 control chromosomes in the GnomAD database, including 4,776 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.073 ( 433 hom., cov: 33)

Exomes 𝑓: 0.071 ( 4343 hom. )

Consequence

AOC1
NM_001091.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039739013).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AOC1	NM_001091.4 linkuse as main transcript	c.995C>T	p.Ser332Phe	missense_variant	2/5	ENST00000360937.9
LOC105375567	XR_928171.3 linkuse as main transcript	n.123-16020G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AOC1	ENST00000360937.9 linkuse as main transcript	c.995C>T	p.Ser332Phe	missense_variant	2/5	1	NM_001091.4	P2	P19801-1

Frequencies

GnomAD3 genomes

AF:

0.0727

AC:

11063

AN:

152194

Hom.:

433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0930

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.0462

Gnomad ASJ

AF:

0.0519

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0279

Gnomad FIN

AF:

0.0650

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.0670

GnomAD3 exomes

AF:

0.0575

AC:

14200

AN:

247160

Hom.:

547

AF XY:

0.0567

AC XY:

7623

AN XY:

134528

show subpopulations

Gnomad AFR exome

AF:

0.0920

Gnomad AMR exome

AF:

0.0301

Gnomad ASJ exome

AF:

0.0482

Gnomad EAS exome

AF:

0.00179

Gnomad SAS exome

AF:

0.0312

Gnomad FIN exome

AF:

0.0711

Gnomad NFE exome

AF:

0.0757

Gnomad OTH exome

AF:

0.0526

GnomAD4 exome

AF:

0.0706

AC:

103135

AN:

1460316

Hom.:

4343

Cov.:

AF XY:

0.0688

AC XY:

49983

AN XY:

726454

show subpopulations

Gnomad4 AFR exome

AF:

0.0920

Gnomad4 AMR exome

AF:

0.0324

Gnomad4 ASJ exome

AF:

0.0511

Gnomad4 EAS exome

AF:

0.000806

Gnomad4 SAS exome

AF:

0.0299

Gnomad4 FIN exome

AF:

0.0729

Gnomad4 NFE exome

AF:

0.0782

Gnomad4 OTH exome

AF:

0.0621

GnomAD4 genome

AF:

0.0726

AC:

11062

AN:

152312

Hom.:

433

Cov.:

AF XY:

0.0697

AC XY:

5188

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0927

Gnomad4 AMR

AF:

0.0461

Gnomad4 ASJ

AF:

0.0519

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0282

Gnomad4 FIN

AF:

0.0650

Gnomad4 NFE

AF:

0.0766

Gnomad4 OTH

AF:

0.0663

Alfa

AF:

0.0702

Hom.:

962

Bravo

AF:

0.0724

TwinsUK

AF:

0.0823

AC:

305

ALSPAC

AF:

0.0732

AC:

282

ESP6500AA

AF:

0.0861

AC:

379

ESP6500EA

AF:

0.0738

AC:

634

ExAC

AF:

0.0591

AC:

7172

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0705

EpiControl

AF:

0.0706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.24

T;T;T;.;T

Eigen

Uncertain

0.33

Eigen_PC

Benign

0.19

FATHMM_MKL

Benign

0.33

LIST_S2

Uncertain

0.89

.;D;.;D;T

MetaRNN

Benign

0.0040

T;T;T;T;T

MetaSVM

Benign

-1.2

MutationAssessor

Pathogenic

3.0

M;M;M;M;.

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-3.0

D;D;D;D;D

REVEL

Benign

0.12

Sift

Uncertain

0.0050

D;D;D;T;D

Sift4G

Uncertain

0.030

D;D;D;D;D

Polyphen

0.99

D;D;D;.;.

Vest4

0.089

MPC

0.83

ClinPred

0.037

GERP RS

5.0

Varity_R

0.51

gMVP

0.70

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