ENST00000580900.5:c.*698G>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000580900.5(MTAP):c.*698G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,040 control chromosomes in the GnomAD database, including 15,259 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.39 ( 15259 hom., cov: 32)
Exomes 𝑓: 0.20 ( 0 hom. )
Consequence
MTAP
ENST00000580900.5 3_prime_UTR
ENST00000580900.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.665
Publications
2 publications found
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 Gene-Disease associations (from GenCC):
- diaphyseal medullary stenosis-bone malignancy syndromeInheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Genomics England PanelApp, G2P, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTAP | NM_001396041.1 | c.*698G>T | 3_prime_UTR_variant | Exon 8 of 8 | NP_001382970.1 | |||
MTAP | NM_001396044.1 | c.922+781G>T | intron_variant | Intron 8 of 9 | NP_001382973.1 | |||
MTAP | NM_001396045.1 | c.799+781G>T | intron_variant | Intron 7 of 8 | NP_001382974.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTAP | ENST00000580900.5 | c.*698G>T | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000463424.1 | ||||
MTAP | ENST00000616982.1 | n.1508G>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
ENSG00000264545 | ENST00000404796.3 | n.461-97536G>T | intron_variant | Intron 4 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.386 AC: 58664AN: 151912Hom.: 15207 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
58664
AN:
151912
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.200 AC: 2AN: 10Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1AN XY: 8 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
10
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
8
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
2
AN:
10
Other (OTH)
AC:
0
AN:
0
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.387 AC: 58784AN: 152030Hom.: 15259 Cov.: 32 AF XY: 0.390 AC XY: 28982AN XY: 74314 show subpopulations
GnomAD4 genome
AF:
AC:
58784
AN:
152030
Hom.:
Cov.:
32
AF XY:
AC XY:
28982
AN XY:
74314
show subpopulations
African (AFR)
AF:
AC:
29837
AN:
41456
American (AMR)
AF:
AC:
6336
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
808
AN:
3470
East Asian (EAS)
AF:
AC:
2804
AN:
5164
South Asian (SAS)
AF:
AC:
1635
AN:
4818
European-Finnish (FIN)
AF:
AC:
2805
AN:
10548
Middle Eastern (MID)
AF:
AC:
71
AN:
294
European-Non Finnish (NFE)
AF:
AC:
13429
AN:
67984
Other (OTH)
AF:
AC:
733
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1439
2878
4317
5756
7195
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
496
992
1488
1984
2480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1618
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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