rs9612234
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002073.4(GNAZ):c.*1462C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,606 control chromosomes in the GnomAD database, including 18,586 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 0.48 ( 18524 hom., cov: 34)
Exomes 𝑓: 0.54 ( 62 hom. )
Consequence
GNAZ
NM_002073.4 3_prime_UTR
NM_002073.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.547
Genes affected
GNAZ (HGNC:4395): (G protein subunit alpha z) The protein encoded by this gene is a member of a G protein subfamily that mediates signal transduction in pertussis toxin-insensitive systms. This encoded protein may play a role in maintaining the ionic balance of perilymphatic and endolymphatic cochlear fluids. [provided by RefSeq, Jul 2008]
RSPH14 (HGNC:13437): (radial spoke head 14 homolog) This gene encodes a protein with no known function but with slight similarity to a yeast vacuolar protein. The gene is located in a region deleted in pediatric rhabdoid tumors of the brain, kidney and soft tissues, but mutations in this gene have not been associated with the disease. [provided by RefSeq, Jul 2008]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAZ | NM_002073.4 | c.*1462C>T | 3_prime_UTR_variant | 3/3 | ENST00000615612.2 | ||
RSPH14 | NM_014433.3 | c.421+9133G>A | intron_variant | ENST00000216036.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAZ | ENST00000615612.2 | c.*1462C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_002073.4 | P1 | ||
RSPH14 | ENST00000216036.9 | c.421+9133G>A | intron_variant | 1 | NM_014433.3 | P1 | |||
RSPH14 | ENST00000421213.1 | c.50-393G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.485 AC: 73722AN: 152016Hom.: 18525 Cov.: 34
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GnomAD4 exome AF: 0.538 AC: 254AN: 472Hom.: 62 Cov.: 0 AF XY: 0.531 AC XY: 152AN XY: 286
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GnomAD4 genome ? AF: 0.485 AC: 73753AN: 152134Hom.: 18524 Cov.: 34 AF XY: 0.482 AC XY: 35885AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
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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