NM_001301267.2:c.28+51A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001301267.2(MT1G):c.28+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,606,400 control chromosomes in the GnomAD database, including 14,989 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 0.11 ( 1030 hom., cov: 33)
Exomes 𝑓: 0.14 ( 13959 hom. )
Consequence
MT1G
NM_001301267.2 intron
NM_001301267.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.715
Publications
9 publications found
Genes affected
MT1G (HGNC:7399): (metallothionein 1G) Enables zinc ion binding activity. Involved in cellular response to metal ion; cellular response to vascular endothelial growth factor stimulus; and negative regulation of growth. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT1G | ENST00000379811.4 | c.28+51A>G | intron_variant | Intron 1 of 2 | 1 | NM_001301267.2 | ENSP00000369139.4 | |||
MT1G | ENST00000444837.6 | c.28+51A>G | intron_variant | Intron 1 of 2 | 1 | ENSP00000391397.2 | ||||
MT1G | ENST00000568675.1 | n.56+51A>G | intron_variant | Intron 1 of 1 | 1 | |||||
MT1G | ENST00000569500.5 | c.28+51A>G | intron_variant | Intron 1 of 1 | 3 | ENSP00000456675.1 |
Frequencies
GnomAD3 genomes AF: 0.105 AC: 15973AN: 152108Hom.: 1030 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
15973
AN:
152108
Hom.:
Cov.:
33
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:
GnomAD2 exomes AF: 0.123 AC: 30974AN: 251382 AF XY: 0.124 show subpopulations
GnomAD2 exomes
AF:
AC:
30974
AN:
251382
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.135 AC: 197003AN: 1454174Hom.: 13959 Cov.: 30 AF XY: 0.135 AC XY: 97547AN XY: 723890 show subpopulations
GnomAD4 exome
AF:
AC:
197003
AN:
1454174
Hom.:
Cov.:
30
AF XY:
AC XY:
97547
AN XY:
723890
show subpopulations
African (AFR)
AF:
AC:
1042
AN:
33318
American (AMR)
AF:
AC:
6471
AN:
44670
Ashkenazi Jewish (ASJ)
AF:
AC:
1484
AN:
26064
East Asian (EAS)
AF:
AC:
3121
AN:
39598
South Asian (SAS)
AF:
AC:
9868
AN:
86090
European-Finnish (FIN)
AF:
AC:
8084
AN:
53226
Middle Eastern (MID)
AF:
AC:
416
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
159492
AN:
1105364
Other (OTH)
AF:
AC:
7025
AN:
60102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
8599
17198
25797
34396
42995
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
5678
11356
17034
22712
28390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.105 AC: 15985AN: 152226Hom.: 1030 Cov.: 33 AF XY: 0.104 AC XY: 7752AN XY: 74416 show subpopulations
GnomAD4 genome
AF:
AC:
15985
AN:
152226
Hom.:
Cov.:
33
AF XY:
AC XY:
7752
AN XY:
74416
show subpopulations
African (AFR)
AF:
AC:
1557
AN:
41556
American (AMR)
AF:
AC:
1786
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
210
AN:
3470
East Asian (EAS)
AF:
AC:
368
AN:
5182
South Asian (SAS)
AF:
AC:
520
AN:
4818
European-Finnish (FIN)
AF:
AC:
1573
AN:
10598
Middle Eastern (MID)
AF:
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
AC:
9638
AN:
67996
Other (OTH)
AF:
AC:
210
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
732
1464
2195
2927
3659
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
182
364
546
728
910
<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:
280
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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