Variant 1-109628106-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001368809.2(AMPD2):c.1104G>A(p.Ser368=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 1,613,870 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 41 hom., cov: 32)

Exomes 𝑓: 0.023 ( 561 hom. )

Consequence

AMPD2
NM_001368809.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -3.70

Variant links:

Genes affected

AMPD2 (HGNC:469): (adenosine monophosphate deaminase 2) The protein encoded by this gene is important in purine metabolism by converting AMP to IMP. The encoded protein, which acts as a homotetramer, is one of three AMP deaminases found in mammals. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

AMPD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 1-109628106-G-A is Benign according to our data. Variant chr1-109628106-G-A is described in ClinVar as [Benign]. Clinvar id is 474994.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-109628106-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-3.7 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMPD2	NM_001368809.2 linkuse as main transcript	c.1104G>A	p.Ser368=	synonymous_variant	11/19	ENST00000528667.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMPD2	ENST00000528667.7 linkuse as main transcript	c.1104G>A	p.Ser368=	synonymous_variant	11/19	1	NM_001368809.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0162

AC:

2472

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00603

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00942

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0588

Gnomad FIN

AF:

0.00735

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0233

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0199

AC:

5002

AN:

251042

Hom.:

AF XY:

0.0222

AC XY:

3010

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.00646

Gnomad AMR exome

AF:

0.00665

Gnomad ASJ exome

AF:

0.0254

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0510

Gnomad FIN exome

AF:

0.00828

Gnomad NFE exome

AF:

0.0226

Gnomad OTH exome

AF:

0.0165

GnomAD4 exome

AF:

0.0234

AC:

34146

AN:

1461548

Hom.:

561

Cov.:

AF XY:

0.0241

AC XY:

17544

AN XY:

727082

show subpopulations

Gnomad4 AFR exome

AF:

0.00496

Gnomad4 AMR exome

AF:

0.00689

Gnomad4 ASJ exome

AF:

0.0251

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0514

Gnomad4 FIN exome

AF:

0.00836

Gnomad4 NFE exome

AF:

0.0240

Gnomad4 OTH exome

AF:

0.0224

GnomAD4 genome

AF:

0.0162

AC:

2469

AN:

152322

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1194

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00601

Gnomad4 AMR

AF:

0.00941

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0580

Gnomad4 FIN

AF:

0.00735

Gnomad4 NFE

AF:

0.0233

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.0176

Hom.:

Bravo

AF:

0.0148

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0243

EpiControl

AF:

0.0233

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spastic paraplegia 63

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 25, 2018

- -

Pontocerebellar hypoplasia type 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

2.1

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over