rs11145958
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080849.3(DNLZ):c.*1391C>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 0.0369 in 152,146 control chromosomes in the GnomAD database, including 139 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 0.037 ( 139 hom., cov: 32)
Exomes 𝑓: 0.043 ( 0 hom. )
Consequence
DNLZ
NM_001080849.3 3_prime_UTR
NM_001080849.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
Genes affected
DNLZ (HGNC:33879): (DNL-type zinc finger) Predicted to enable chaperone binding activity. Predicted to be involved in protein folding; protein import into mitochondrial matrix; and protein stabilization. Located in mitochondrion and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNLZ | NM_001080849.3 | c.*1391C>T | 3_prime_UTR_variant | 3/3 | ENST00000371738.4 | ||
DNLZ | NR_073565.2 | n.1962C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNLZ | ENST00000371738.4 | c.*1391C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_001080849.3 | P1 | ||
DNLZ | ENST00000371739.3 | c.*1434C>T | 3_prime_UTR_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0369 AC: 5604AN: 151982Hom.: 139 Cov.: 32
GnomAD3 genomes
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151982
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32
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GnomAD4 exome AF: 0.0435 AC: 2AN: 46Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 2AN XY: 36
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GnomAD4 genome ? AF: 0.0369 AC: 5614AN: 152100Hom.: 139 Cov.: 32 AF XY: 0.0369 AC XY: 2743AN XY: 74362
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at