6-94446700-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000404146.1(MTCYBP36):n.*40G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,026 control chromosomes in the GnomAD database, including 2,703 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 0.17 ( 2703 hom., cov: 32)
Exomes 𝑓: 0.19 ( 0 hom. )
Consequence
MTCYBP36
ENST00000404146.1 downstream_gene
ENST00000404146.1 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.393
Publications
6 publications found
Genes affected
Genome browser will be placed here
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MTCYBP36 | ENST00000404146.1 | n.*40G>A | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes 0.167 AC: 25302AN: 151892Hom.: 2703 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
25302
AN:
151892
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: 0.188 AC: 3AN: 16Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3AN XY: 10 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
16
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
10
show subpopulations
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:
3
AN:
16
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
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 0.166 AC: 25289AN: 152010Hom.: 2703 Cov.: 32 AF XY: 0.163 AC XY: 12085AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
25289
AN:
152010
Hom.:
Cov.:
32
AF XY:
AC XY:
12085
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
2425
AN:
41508
American (AMR)
AF:
AC:
2773
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
820
AN:
3470
East Asian (EAS)
AF:
AC:
70
AN:
5148
South Asian (SAS)
AF:
AC:
394
AN:
4804
European-Finnish (FIN)
AF:
AC:
2049
AN:
10558
Middle Eastern (MID)
AF:
AC:
48
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16016
AN:
67936
Other (OTH)
AF:
AC:
366
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1019
2038
3058
4077
5096
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
266
532
798
1064
1330
<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:
175
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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