rs3812552
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080849.3(DNLZ):āc.533G>Cā(p.Ser178Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,313,490 control chromosomes in the GnomAD database, including 7,493 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001080849.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNLZ | NM_001080849.3 | c.533G>C | p.Ser178Thr | missense_variant | 3/3 | ENST00000371738.4 | |
DNLZ | NR_073565.2 | n.567G>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNLZ | ENST00000371738.4 | c.533G>C | p.Ser178Thr | missense_variant | 3/3 | 1 | NM_001080849.3 | P1 | |
DNLZ | ENST00000371739.3 | c.*39G>C | 3_prime_UTR_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0769 AC: 11706AN: 152204Hom.: 584 Cov.: 34
GnomAD3 exomes AF: 0.0850 AC: 6186AN: 72812Hom.: 274 AF XY: 0.0841 AC XY: 3293AN XY: 39148
GnomAD4 exome AF: 0.107 AC: 123997AN: 1161168Hom.: 6906 Cov.: 31 AF XY: 0.106 AC XY: 59194AN XY: 557858
GnomAD4 genome ? AF: 0.0769 AC: 11710AN: 152322Hom.: 587 Cov.: 34 AF XY: 0.0750 AC XY: 5584AN XY: 74478
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at