rs746759188
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PVS1_ModerateBS2
The ENST00000251038.10(ZC3H14):c.1851_1868+13delCCCCATCTCACCCTGCAAGTGAGTACCATCC(p.His617_Lys623delinsGln) variant causes a splice donor, disruptive inframe deletion, splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,460,054 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000251038.10 splice_donor, disruptive_inframe_deletion, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZC3H14 | ENST00000251038.10 | c.1851_1868+13delCCCCATCTCACCCTGCAAGTGAGTACCATCC | p.His617_Lys623delinsGln | splice_donor_variant, disruptive_inframe_deletion, splice_region_variant, intron_variant | Exon 13 of 17 | 1 | NM_024824.5 | ENSP00000251038.5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 196AN: 150206Hom.: 1 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.000430 AC: 108AN: 251192Hom.: 0 AF XY: 0.000309 AC XY: 42AN XY: 135748
GnomAD4 exome AF: 0.000195 AC: 285AN: 1460054Hom.: 2 AF XY: 0.000191 AC XY: 139AN XY: 726310
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00130 AC: 195AN: 150322Hom.: 1 Cov.: 31 AF XY: 0.00118 AC XY: 87AN XY: 73456
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at