9-21816759-G-A

Position:

chr9-21816759-G-A

Variant summary

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

The NM_002451.4(MTAP):c.166G>A(p.Val56Ile) variant causes a missense change. The variant allele was found at a frequency of 0.407 in 1,605,850 control chromosomes in the GnomAD database, including 136,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 13300 hom., cov: 31)

Exomes 𝑓: 0.41 ( 123052 hom. )

Consequence

MTAP
NM_002451.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 6.67

Variant links:

Genes affected

MTAP (HGNC:7413): (methylthioadenosine phosphorylase) This gene encodes an enzyme that plays a major role in polyamine metabolism and is important for the salvage pathway of both adenine and methionine. The encoded enzyme is deficient in many cancers. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2021]

MTAP 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 (MetaRNN=0.0035783052).

BP6

Variant 9-21816759-G-A is Benign according to our data. Variant chr9-21816759-G-A is described in ClinVar as [Benign]. Clinvar id is 366238.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTAP	NM_002451.4 linkuse as main transcript	c.166G>A	p.Val56Ile	missense_variant	3/8	ENST00000644715.2	NP_002442.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTAP	ENST00000644715.2 linkuse as main transcript	c.166G>A	p.Val56Ile	missense_variant	3/8		NM_002451.4	ENSP00000494373	P1	Q13126-1

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63154

AN:

151810

Hom.:

13290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.394

GnomAD3 exomes

AF:

0.397

AC:

98297

AN:

247862

Hom.:

20353

AF XY:

0.385

AC XY:

51560

AN XY:

134030

show subpopulations

Gnomad AFR exome

AF:

0.436

Gnomad AMR exome

AF:

0.416

Gnomad ASJ exome

AF:

0.379

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.435

Gnomad NFE exome

AF:

0.413

Gnomad OTH exome

AF:

0.385

GnomAD4 exome

AF:

0.406

AC:

591018

AN:

1453922

Hom.:

123052

Cov.:

AF XY:

0.400

AC XY:

289460

AN XY:

723284

show subpopulations

Gnomad4 AFR exome

AF:

0.431

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.383

Gnomad4 EAS exome

AF:

0.405

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.430

Gnomad4 NFE exome

AF:

0.419

Gnomad4 OTH exome

AF:

0.394

GnomAD4 genome

AF:

0.416

AC:

63217

AN:

151928

Hom.:

13300

Cov.:

AF XY:

0.412

AC XY:

30603

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.444

Gnomad4 SAS

AF:

0.239

Gnomad4 FIN

AF:

0.416

Gnomad4 NFE

AF:

0.419

Gnomad4 OTH

AF:

0.398

Alfa

AF:

0.408

Hom.:

27887

Bravo

AF:

0.421

TwinsUK

AF:

0.415

AC:

1540

ALSPAC

AF:

0.415

AC:

1601

ESP6500AA

AF:

0.435

AC:

1916

ESP6500EA

AF:

0.415

AC:

3569

ExAC

AF:

0.394

AC:

47881

Asia WGS

AF:

0.327

AC:

1138

AN:

3478

EpiCase

AF:

0.395

EpiControl

AF:

0.387

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Diaphyseal medullary stenosis-bone malignancy syndrome

Benign:3

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.14

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.44

T;T;T;.

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.76

.;T;T;T

MetaRNN

Benign

0.0036

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

M;.;M;M

MutationTaster

Benign

1.1e-10

P;P;P

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-0.82

N;.;.;.

REVEL

Uncertain

0.49

Sift

Benign

0.13

T;.;.;.

Sift4G

Benign

0.13

T;T;.;T

Polyphen

0.0060

B;B;B;.

Vest4

0.10

MPC

0.11

ClinPred

0.033

GERP RS

5.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.37

gMVP

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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