chr7-2720161-C-T

Variant names:

• chr7-2720161-C-T
• rs798554
• ENST00000489665.1:n.550+10345C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384740.1(AMZ1):​c.948+10345C>T variant causes a intron 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 NM_001384740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384740.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMZ1	NM_001384740.1		c.948+10345C>T		intron	N/A	NP_001371669.1
	AMZ1	NM_001321766.2		c.948+10345C>T		intron	N/A	NP_001308695.1
	AMZ1	NM_001384742.1		c.779-4320C>T		intron	N/A	NP_001371671.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMZ1	ENST00000489665.1	TSL:1	n.550+10345C>T		intron	N/A

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

African (AFR) AF: 0.143 AC: 5926 AN: 41486

American (AMR) AF: 0.284 AC: 4332 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1128 AN: 5172

South Asian (SAS) AF: 0.155 AC: 749 AN: 4824

European-Finnish (FIN) AF: 0.384 AC: 4061 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19925 AN: 67726

Other (OTH) AF: 0.252 AC: 532 AN: 2114

Alfa AF: 0.273 Hom.: 9515

Bravo AF: 0.238

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs798554; hg19: chr7-2759795;