rs7120076
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001100388.2(HOATZ):c.399+154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0363 in 152,322 control chromosomes in the GnomAD database, including 345 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.036 ( 345 hom., cov: 33)
Consequence
HOATZ
NM_001100388.2 intron
NM_001100388.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.592
Genes affected
HOATZ (HGNC:25061): (HOATZ cilia and flagella associated protein) Predicted to be involved in axoneme assembly; flagellated sperm motility; and spermatogenesis. Predicted to be located in cilium and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOATZ | NM_001100388.2 | c.399+154A>G | intron_variant | ENST00000375618.9 | |||
HOATZ | NM_207430.2 | c.480+154A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOATZ | ENST00000375618.9 | c.399+154A>G | intron_variant | 1 | NM_001100388.2 | P1 | |||
HOATZ | ENST00000332814.6 | c.480+154A>G | intron_variant | 5 | |||||
HOATZ | ENST00000529167.5 | c.480+154A>G | intron_variant | 2 | |||||
HOATZ | ENST00000529661.1 | c.*219+154A>G | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0362 AC: 5513AN: 152204Hom.: 343 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0363 AC: 5530AN: 152322Hom.: 345 Cov.: 33 AF XY: 0.0357 AC XY: 2662AN XY: 74494
GnomAD4 genome
?
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AC:
5530
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152322
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33
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2662
AN XY:
74494
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33
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at