rs798554

chr7-2720161-C-T

Variant summary

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

The ENST00000489665.1(AMZ1):n.550+10345C>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 0.249 in 151,804 control chromosomes in the GnomAD database, including 5,247 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 0.25 (5247 hom., cov: 32)
• Consequence: AMZ1 ENST00000489665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

AMZ1 (HGNC:22231): (archaelysin family metallopeptidase 1) Predicted to enable metal ion binding activity and metallopeptidase activity. Predicted to be involved in proteolysis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMZ1	NM_001321766.2	c.948+10345C>T		intron_variant
AMZ1	NM_001384740.1	c.948+10345C>T		intron_variant
AMZ1	NM_001384741.1	c.778+10345C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMZ1	ENST00000489665.1	n.550+10345C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37852 AN: 151686 Hom.: 5245 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37863 AN: 151804 Hom.: 5247 Cov.: 32 AF XY: 0.252 AC XY: 18716 AN XY: 74234

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.252

Alfa AF: 0.258 Hom.: 913

Bravo AF: 0.238

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.4
Dann	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs798554; hg19: chr7-2759795;