Variant chr1-109620296-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001368809.2(AMPD2):c.-263+18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 1,612,938 control chromosomes in the GnomAD database, including 9,248 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1101 hom., cov: 32)

Exomes 𝑓: 0.083 ( 8147 hom. )

Consequence

AMPD2
NM_001368809.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.150

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-109620296-T-C is Benign according to our data. Variant chr1-109620296-T-C is described in ClinVar as [Benign]. Clinvar id is 1255291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMPD2	NM_001368809.2 linkuse as main transcript	c.-263+18T>C		intron_variant		ENST00000528667.7	NP_001355738.1
AMPD2	NM_139156.4 linkuse as main transcript	c.10+18T>C		intron_variant			NP_631895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMPD2	ENST00000528667.7 linkuse as main transcript	c.-263+18T>C		intron_variant		1	NM_001368809.2	ENSP00000436541	P1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15340

AN:

151756

Hom.:

1103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.0574

Gnomad AMR

AF:

0.0719

Gnomad ASJ

AF:

0.0708

Gnomad EAS

AF:

0.313

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.0587

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0580

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.110

AC:

27577

AN:

250810

Hom.:

2576

AF XY:

0.115

AC XY:

15634

AN XY:

135530

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.0605

Gnomad ASJ exome

AF:

0.0801

Gnomad EAS exome

AF:

0.312

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.0542

Gnomad NFE exome

AF:

0.0575

Gnomad OTH exome

AF:

0.0908

GnomAD4 exome

AF:

0.0825

AC:

120567

AN:

1461064

Hom.:

8147

Cov.:

AF XY:

0.0873

AC XY:

63472

AN XY:

726786

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.0623

Gnomad4 ASJ exome

AF:

0.0791

Gnomad4 EAS exome

AF:

0.283

Gnomad4 SAS exome

AF:

0.265

Gnomad4 FIN exome

AF:

0.0561

Gnomad4 NFE exome

AF:

0.0597

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.101

AC:

15353

AN:

151874

Hom.:

1101

Cov.:

AF XY:

0.106

AC XY:

7846

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.150

Gnomad4 AMR

AF:

0.0719

Gnomad4 ASJ

AF:

0.0708

Gnomad4 EAS

AF:

0.312

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.0587

Gnomad4 NFE

AF:

0.0580

Gnomad4 OTH

AF:

0.107

Alfa

AF:

0.0761

Hom.:

176

Bravo

AF:

0.100

Asia WGS

AF:

0.263

AC:

914

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 06, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hereditary spastic paraplegia 63

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

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

-0.86

CADD

Benign

9.3

DANN

Benign

0.71

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