rs34030799

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001368809.2(AMPD2):c.1104G>A(p.Ser368Ser) 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:5

Conservation

PhyloP100: -3.70

Publications

5 publications found

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 Gene-Disease associations (from GenCC):

pontocerebellar hypoplasia type 9
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P, Ambry Genetics
hereditary spastic paraplegia 63
Inheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

AMPD2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.047).

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.

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 rank	MANE	Protein	UniProt
AMPD2	NM_001368809.2 link	c.1104G>A	p.Ser368Ser	synonymous_variant	Exon 11 of 19	ENST00000528667.7	NP_001355738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMPD2	ENST00000528667.7 link	c.1104G>A	p.Ser368Ser	synonymous_variant	Exon 11 of 19	1	NM_001368809.2	ENSP00000436541.2

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

GnomAD2 exomes

AF:

0.0199

AC:

5002

AN:

251042

AF XY:

0.0222

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 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

African (AFR)

AF:

0.00496

AC:

166

AN:

33478

American (AMR)

AF:

0.00689

AC:

308

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.0251

AC:

655

AN:

26126

East Asian (EAS)

AF:

0.000126

AC:

AN:

39698

South Asian (SAS)

AF:

0.0514

AC:

4431

AN:

86238

European-Finnish (FIN)

AF:

0.00836

AC:

445

AN:

53250

Middle Eastern (MID)

AF:

0.0237

AC:

136

AN:

5748

European-Non Finnish (NFE)

AF:

0.0240

AC:

26647

AN:

1111906

Other (OTH)

AF:

0.0224

AC:

1353

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

1944

3888

5831

7775

9719

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0162

AC:

2469

AN:

152322

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1194

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.00601

AC:

250

AN:

41566

American (AMR)

AF:

0.00941

AC:

144

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0239

AC:

AN:

3472

East Asian (EAS)

AF:

0.000965

AC:

AN:

5184

South Asian (SAS)

AF:

0.0580

AC:

280

AN:

4828

European-Finnish (FIN)

AF:

0.00735

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0233

AC:

1583

AN:

68034

Other (OTH)

AF:

0.0132

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

125

250

375

500

625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0179

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:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Aug 25, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Hereditary spastic paraplegia 63

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9

Benign:1

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Pontocerebellar hypoplasia type 9

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

2.1

(source)

DANN

Benign

0.84

PhyloP100

-3.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs34030799

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over