17-15999509-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001042697.2(ZSWIM7):c.76+10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,598,176 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001042697.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSWIM7 | NM_001042697.2 | c.76+10C>G | intron_variant | Intron 1 of 4 | ENST00000399277.6 | NP_001036162.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000664 AC: 101AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000743 AC: 162AN: 217908Hom.: 0 AF XY: 0.000842 AC XY: 102AN XY: 121208
GnomAD4 exome AF: 0.00105 AC: 1513AN: 1445892Hom.: 3 Cov.: 31 AF XY: 0.00110 AC XY: 792AN XY: 719484
GnomAD4 genome AF: 0.000663 AC: 101AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74458
ClinVar
Submissions by phenotype
Mitochondrial complex III deficiency nuclear type 1 Uncertain:1
- -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at