17-15999502-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001042697.2(ZSWIM7):c.76+17G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00619 in 1,596,822 control chromosomes in the GnomAD database, including 502 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001042697.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSWIM7 | NM_001042697.2 | c.76+17G>T | intron_variant | Intron 1 of 4 | ENST00000399277.6 | NP_001036162.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0321 AC: 4878AN: 152190Hom.: 261 Cov.: 32
GnomAD3 exomes AF: 0.00782 AC: 1690AN: 215988Hom.: 77 AF XY: 0.00554 AC XY: 667AN XY: 120296
GnomAD4 exome AF: 0.00345 AC: 4990AN: 1444514Hom.: 237 Cov.: 31 AF XY: 0.00297 AC XY: 2137AN XY: 718752
GnomAD4 genome AF: 0.0322 AC: 4900AN: 152308Hom.: 265 Cov.: 32 AF XY: 0.0306 AC XY: 2281AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
Mitochondrial complex III deficiency nuclear type 1 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at