7-150858827-A-G

Position:

• chr7-150858827-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001091.4(AOC1):​c.1635A>G​(p.Pro545=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,612,818 control chromosomes in the GnomAD database, including 97,321 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 0.38 (11842 hom., cov: 32)
  • Exomes 𝑓: 0.33 (85479 hom.)
• Consequence: AOC1 NM_001091.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.31

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]

LOC105375567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-4.31 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOC1	NM_001091.4	c.1635A>G	p.Pro545=	synonymous_variant	3/5	ENST00000360937.9	NP_001082.2
LOC105375567	XR_928171.3	n.123-17382T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9	c.1635A>G	p.Pro545=	synonymous_variant	3/5	1	NM_001091.4	ENSP00000354193	P2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58058 AN: 151852 Hom.: 11832 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.358

GnomAD3 exomes AF: 0.375 AC: 93370 AN: 248826 Hom.: 18678 AF XY: 0.374 AC XY: 50453 AN XY: 135036

Gnomad AFR exome AF: 0.498

Gnomad AMR exome AF: 0.425

Gnomad ASJ exome AF: 0.390

Gnomad EAS exome AF: 0.504

Gnomad SAS exome AF: 0.490

Gnomad FIN exome AF: 0.325

Gnomad NFE exome AF: 0.301

Gnomad OTH exome AF: 0.345

GnomAD4 exome AF: 0.332 AC: 485414 AN: 1460848 Hom.: 85479 Cov.: 53 AF XY: 0.336 AC XY: 244130 AN XY: 726596

Gnomad4 AFR exome AF: 0.501

Gnomad4 AMR exome AF: 0.423

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.538

Gnomad4 SAS exome AF: 0.490

Gnomad4 FIN exome AF: 0.323

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.349

GnomAD4 genome AF: 0.382 AC: 58102 AN: 151970 Hom.: 11842 Cov.: 32 AF XY: 0.384 AC XY: 28511 AN XY: 74296

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.358

Alfa AF: 0.316 Hom.: 16092

Bravo AF: 0.392

Asia WGS AF: 0.470 AC: 1631 AN: 3478

EpiCase AF: 0.300

EpiControl AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs10893; hg19: chr7-150555915; COSMIC: COSV62869446; COSMIC: COSV62869446;