Variant rs798470 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001384743.1(AMZ1):c.305-259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 490,732 control chromosomes in the GnomAD database, including 92,353 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 0.66 ( 35444 hom., cov: 34)

Exomes 𝑓: 0.57 ( 56909 hom. )

Consequence

AMZ1
NM_001384743.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Variant links:

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]

AMZ1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMZ1	NM_001384743.1 link	c.305-259T>C		intron_variant		ENST00000683327.1	NP_001371672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMZ1	ENST00000683327.1 link	c.305-259T>C		intron_variant			NM_001384743.1	ENSP00000506962.1		Q400G9-1

Frequencies

GnomAD3 genomes

AF:

0.664

AC:

101041

AN:

152088

Hom.:

35372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.895

Gnomad AMI

AF:

0.622

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.593

Gnomad OTH

AF:

0.648

GnomAD4 exome

AF:

0.569

AC:

192768

AN:

338526

Hom.:

56909

Cov.:

AF XY:

0.563

AC XY:

98497

AN XY:

174800

show subpopulations

Gnomad4 AFR exome

AF:

0.893

Gnomad4 AMR exome

AF:

0.546

Gnomad4 ASJ exome

AF:

0.497

Gnomad4 EAS exome

AF:

0.333

Gnomad4 SAS exome

AF:

0.464

Gnomad4 FIN exome

AF:

0.672

Gnomad4 NFE exome

AF:

0.587

Gnomad4 OTH exome

AF:

0.581

GnomAD4 genome

AF:

0.665

AC:

101173

AN:

152206

Hom.:

35444

Cov.:

AF XY:

0.661

AC XY:

49171

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.896

Gnomad4 AMR

AF:

0.569

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.467

Gnomad4 FIN

AF:

0.685

Gnomad4 NFE

AF:

0.593

Gnomad4 OTH

AF:

0.651

Alfa

AF:

0.622

Hom.:

6251

Bravo

AF:

0.666

Asia WGS

AF:

0.495

AC:

1723

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.0

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over