7-150858914-T-C

Position:

• chr7-150858914-T-C

Variant summary

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

The NM_001091.4(AOC1):​c.1722T>C​(p.Pro574=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,611,814 control chromosomes in the GnomAD database, including 152,560 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 0.47 (16792 hom., cov: 32)
  • Exomes 𝑓: 0.43 (135768 hom.)
• Consequence: AOC1 NM_001091.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

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=-0.55).
• BP7: Synonymous conserved (PhyloP=0.531 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AOC1	NM_001091.4	c.1722T>C	p.Pro574=	synonymous_variant	3/5	ENST00000360937.9	NP_001082.2
LOC105375567	XR_928171.3	n.123-17469A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000360937.9	c.1722T>C	p.Pro574=	synonymous_variant	3/5	1	NM_001091.4	ENSP00000354193	P2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70664 AN: 151764 Hom.: 16755 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.452

GnomAD3 exomes AF: 0.459 AC: 112498 AN: 245058 Hom.: 26290 AF XY: 0.458 AC XY: 60995 AN XY: 133102

Gnomad AFR exome AF: 0.552

Gnomad AMR exome AF: 0.498

Gnomad ASJ exome AF: 0.466

Gnomad EAS exome AF: 0.580

Gnomad SAS exome AF: 0.509

Gnomad FIN exome AF: 0.431

Gnomad NFE exome AF: 0.407

Gnomad OTH exome AF: 0.440

GnomAD4 exome AF: 0.427 AC: 622815 AN: 1459932 Hom.: 135768 Cov.: 75 AF XY: 0.430 AC XY: 311890 AN XY: 726104

Gnomad4 AFR exome AF: 0.546

Gnomad4 AMR exome AF: 0.496

Gnomad4 ASJ exome AF: 0.461

Gnomad4 EAS exome AF: 0.612

Gnomad4 SAS exome AF: 0.509

Gnomad4 FIN exome AF: 0.424

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 0.441

GnomAD4 genome AF: 0.466 AC: 70764 AN: 151882 Hom.: 16792 Cov.: 32 AF XY: 0.469 AC XY: 34811 AN XY: 74208

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.457

Alfa AF: 0.424 Hom.: 16374

Bravo AF: 0.473

Asia WGS AF: 0.545 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	6.6
DANN	Benign	0.54

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: rs1049748; hg19: chr7-150556002;