rs6977381

Positions:

• chr7-150845558-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928171.3(LOC105375567):​n.123-4113C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,078 control chromosomes in the GnomAD database, including 33,838 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 0.65 (33838 hom., cov: 32)
• Consequence: LOC105375567 XR_928171.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

Genes affected

LOC105375567 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375567	XR_928171.3	n.123-4113C>T		intron_variant, non_coding_transcript_variant
LOC105375567	XR_928169.3	n.123-4113C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AOC1	ENST00000467291.5	c.-92-6557G>A		intron_variant		5		ENSP00000418328	P2
AOC1	ENST00000493429.5	c.-92-6557G>A		intron_variant		5		ENSP00000418614	P2

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99498 AN: 151960 Hom.: 33789 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.655 AC: 99605 AN: 152078 Hom.: 33838 Cov.: 32 AF XY: 0.658 AC XY: 48932 AN XY: 74328

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.603

Alfa AF: 0.568 Hom.: 51628

Bravo AF: 0.668

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51

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: rs6977381; hg19: chr7-150542646;