Variant chr1-15583355-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_024758.5(AGMAT):c.313G>C(p.Gly105Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 1,613,286 control chromosomes in the GnomAD database, including 266,065 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.65 ( 33358 hom., cov: 32)

Exomes 𝑓: 0.56 ( 232707 hom. )

Consequence

AGMAT
NM_024758.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.615

Variant links:

Genes affected

AGMAT (HGNC:18407): (agmatinase (putative)) Predicted to enable agmatinase activity. Predicted to be involved in putrescine biosynthetic process from arginine, using agmatinase. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

AGMAT links:

DNAJC16 (HGNC:29157): (DnaJ heat shock protein family (Hsp40) member C16) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC16 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 (MetaRNN=6.654469E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGMAT	NM_024758.5 linkuse as main transcript	c.313G>C	p.Gly105Arg	missense_variant	2/7	ENST00000375826.4	NP_079034.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGMAT	ENST00000375826.4 linkuse as main transcript	c.313G>C	p.Gly105Arg	missense_variant	2/7	1	NM_024758.5	ENSP00000364986	P1
DNAJC16	ENST00000483270.1 linkuse as main transcript	n.2726+7883C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.646

AC:

98213

AN:

152030

Hom.:

33306

Cov.:

show subpopulations

Gnomad AFR

AF:

0.858

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.598

GnomAD3 exomes

AF:

0.558

AC:

140007

AN:

250720

Hom.:

40781

AF XY:

0.550

AC XY:

74607

AN XY:

135548

show subpopulations

Gnomad AFR exome

AF:

0.860

Gnomad AMR exome

AF:

0.422

Gnomad ASJ exome

AF:

0.509

Gnomad EAS exome

AF:

0.631

Gnomad SAS exome

AF:

0.438

Gnomad FIN exome

AF:

0.668

Gnomad NFE exome

AF:

0.562

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.560

AC:

817540

AN:

1461138

Hom.:

232707

Cov.:

AF XY:

0.556

AC XY:

403884

AN XY:

726902

show subpopulations

Gnomad4 AFR exome

AF:

0.864

Gnomad4 AMR exome

AF:

0.434

Gnomad4 ASJ exome

AF:

0.517

Gnomad4 EAS exome

AF:

0.622

Gnomad4 SAS exome

AF:

0.440

Gnomad4 FIN exome

AF:

0.662

Gnomad4 NFE exome

AF:

0.558

Gnomad4 OTH exome

AF:

0.571

GnomAD4 genome

AF:

0.646

AC:

98314

AN:

152148

Hom.:

33358

Cov.:

AF XY:

0.645

AC XY:

47996

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.858

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.623

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.564

Gnomad4 OTH

AF:

0.594

Alfa

AF:

0.578

Hom.:

8369

Bravo

AF:

0.645

TwinsUK

AF:

0.552

AC:

2048

ALSPAC

AF:

0.558

AC:

2151

ESP6500AA

AF:

0.851

AC:

3749

ESP6500EA

AF:

0.553

AC:

4755

ExAC

AF:

0.566

AC:

68685

Asia WGS

AF:

0.561

AC:

1952

AN:

3478

EpiCase

AF:

0.547

EpiControl

AF:

0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

8.8

DANN

Benign

0.64

DEOGEN2

Benign

0.069

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.35

MetaRNN

Benign

6.7e-7

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.99

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.51

PROVEAN

Benign

5.3

REVEL

Benign

0.25

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.063

MutPred

0.41

Gain of MoRF binding (P = 0.0106);

MPC

0.36

ClinPred

0.0018

GERP RS

-1.4

Varity_R

0.15

gMVP

0.74

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