chr22-42132027-C-CTT
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The ENST00000439129.5(NDUFA6-DT):n.1719-4172_1719-4171insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 122,380 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0012 ( 4 hom., cov: 27)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NDUFA6-DT
ENST00000439129.5 intron
ENST00000439129.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
Publications
0 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 4 gene
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 |
---|---|---|---|---|---|---|---|---|---|---|
NDUFA6-DT | ENST00000439129.5 | n.1719-4172_1719-4171insTT | intron_variant | Intron 5 of 6 | 5 | |||||
NDUFA6-DT | ENST00000617009.4 | n.-4_-3insTT | upstream_gene_variant | 5 | ||||||
NDUFA6-DT | ENST00000621190.1 | n.-4_-3insTT | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00119 AC: 146AN: 122394Hom.: 4 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
146
AN:
122394
Hom.:
Cov.:
27
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
4
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
2
African (AFR)
AF:
AC:
0
AN:
2
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:
0
AN:
2
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome AF: 0.00119 AC: 146AN: 122380Hom.: 4 Cov.: 27 AF XY: 0.00131 AC XY: 75AN XY: 57452 show subpopulations
GnomAD4 genome
AF:
AC:
146
AN:
122380
Hom.:
Cov.:
27
AF XY:
AC XY:
75
AN XY:
57452
show subpopulations
African (AFR)
AF:
AC:
111
AN:
31338
American (AMR)
AF:
AC:
4
AN:
11430
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3242
East Asian (EAS)
AF:
AC:
1
AN:
4450
South Asian (SAS)
AF:
AC:
1
AN:
3866
European-Finnish (FIN)
AF:
AC:
2
AN:
4900
Middle Eastern (MID)
AF:
AC:
0
AN:
232
European-Non Finnish (NFE)
AF:
AC:
24
AN:
60432
Other (OTH)
AF:
AC:
3
AN:
1684
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.414
Heterozygous variant carriers
0
6
12
17
23
29
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
2
4
6
8
10
<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.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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