Variant chr1-109619926-C-T 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.-615C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 364,084 control chromosomes in the GnomAD database, including 4,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 2092 hom., cov: 33)

Exomes 𝑓: 0.11 ( 2170 hom. )

Consequence

AMPD2
NM_001368809.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.546

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:

GNAT2 (HGNC:4394): (G protein subunit alpha transducin 2) Transducin is a 3-subunit guanine nucleotide-binding protein (G protein) which stimulates the coupling of rhodopsin and cGMP-phoshodiesterase during visual impulses. The transducin alpha subunits in rods and cones are encoded by separate genes. This gene encodes the alpha subunit in cones. [provided by RefSeq, Jul 2008]

GNAT2 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=-0.74).

BP6

Variant 1-109619926-C-T is Benign according to our data. Variant chr1-109619926-C-T is described in ClinVar as [Benign]. Clinvar id is 1256631.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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.-615C>T		5_prime_UTR_variant	1/19	ENST00000528667.7
AMPD2	NM_139156.4 linkuse as main transcript	c.-343C>T		5_prime_UTR_variant	1/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMPD2	ENST00000528667.7 linkuse as main transcript	c.-615C>T		5_prime_UTR_variant	1/19	1	NM_001368809.2	P1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20363

AN:

152126

Hom.:

2093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0830

Gnomad ASJ

AF:

0.0726

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.0567

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.0579

Gnomad OTH

AF:

0.127

GnomAD4 exome

AF:

0.107

AC:

22760

AN:

211838

Hom.:

2170

Cov.:

AF XY:

0.124

AC XY:

14337

AN XY:

115402

show subpopulations

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.0700

Gnomad4 ASJ exome

AF:

0.0741

Gnomad4 EAS exome

AF:

0.261

Gnomad4 SAS exome

AF:

0.256

Gnomad4 FIN exome

AF:

0.0513

Gnomad4 NFE exome

AF:

0.0551

Gnomad4 OTH exome

AF:

0.0968

GnomAD4 genome

AF:

0.134

AC:

20389

AN:

152246

Hom.:

2092

Cov.:

AF XY:

0.136

AC XY:

10139

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.265

Gnomad4 AMR

AF:

0.0829

Gnomad4 ASJ

AF:

0.0726

Gnomad4 EAS

AF:

0.311

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.0567

Gnomad4 NFE

AF:

0.0579

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.0985

Hom.:

170

Bravo

AF:

0.138

Asia WGS

AF:

0.269

AC:

935

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

9.3

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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