rs772015167
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_022095.4(ZNF335):c.3670-8A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,406,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022095.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF335 | NM_022095.4 | c.3670-8A>C | splice_region_variant, intron_variant | Intron 24 of 27 | ENST00000322927.3 | NP_071378.1 | ||
ZNF335 | XM_047440363.1 | c.3670-8A>C | splice_region_variant, intron_variant | Intron 23 of 26 | XP_047296319.1 | |||
ZNF335 | XM_005260504.5 | c.3667-8A>C | splice_region_variant, intron_variant | Intron 23 of 26 | XP_005260561.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 12AN: 150034Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000700 AC: 15AN: 214316Hom.: 0 AF XY: 0.0000343 AC XY: 4AN XY: 116506
GnomAD4 exome AF: 0.0000434 AC: 61AN: 1406332Hom.: 0 Cov.: 31 AF XY: 0.0000429 AC XY: 30AN XY: 699372
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000800 AC: 12AN: 150034Hom.: 0 Cov.: 32 AF XY: 0.0000820 AC XY: 6AN XY: 73132
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 03, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 14, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at