22-42126390-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000439129.5(NDUFA6-DT):​n.1718+983G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 648,100 control chromosomes in the GnomAD database, including 17,575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.19 ( 3782 hom., cov: 32)
Exomes 𝑓: 0.21 ( 13793 hom. )

Consequence

NDUFA6-DT
ENST00000439129.5 intron

Scores

2

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 0.151
Variant links:
Genes affected
NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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
NDUFA6-DTENST00000439129.5 linkn.1718+983G>A intron_variant Intron 5 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.189
AC:
28373
AN:
150378
Hom.:
3786
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.295
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.246
Gnomad EAS
AF:
0.512
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.114
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.222
Gnomad OTH
AF:
0.178
GnomAD4 exome
AF:
0.211
AC:
105074
AN:
497606
Hom.:
13793
AF XY:
0.210
AC XY:
53900
AN XY:
256990
show subpopulations
Gnomad4 AFR exome
AF:
0.125
Gnomad4 AMR exome
AF:
0.135
Gnomad4 ASJ exome
AF:
0.242
Gnomad4 EAS exome
AF:
0.441
Gnomad4 SAS exome
AF:
0.150
Gnomad4 FIN exome
AF:
0.119
Gnomad4 NFE exome
AF:
0.215
Gnomad4 OTH exome
AF:
0.204
GnomAD4 genome
AF:
0.188
AC:
28356
AN:
150494
Hom.:
3782
Cov.:
32
AF XY:
0.183
AC XY:
13467
AN XY:
73488
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.152
Gnomad4 ASJ
AF:
0.246
Gnomad4 EAS
AF:
0.512
Gnomad4 SAS
AF:
0.165
Gnomad4 FIN
AF:
0.114
Gnomad4 NFE
AF:
0.222
Gnomad4 OTH
AF:
0.175
Alfa
AF:
0.107
Hom.:
194
Bravo
AF:
0.191
Asia WGS
AF:
0.285
AC:
986
AN:
3456

ClinVar

Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Tramadol response Other:1
Apr 28, 2018
Bruce Budowle Laboratory, University of North Texas Health Science Center
Significance: drug response
Review Status: no assertion criteria provided
Collection Method: research

- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.6
DANN
Benign
0.35

Splicing

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.

Other links and lift over

dbSNP: rs28371738; hg19: chr22-42522392; API