NM_002073.4:c.*1462C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
Publications
3 publications found
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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNAZ | ENST00000615612.2 | c.*1462C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_002073.4 | ENSP00000478892.1 | |||
RSPH14 | ENST00000216036.9 | c.421+9133G>A | intron_variant | Intron 4 of 6 | 1 | NM_014433.3 | ENSP00000216036.4 | |||
RSPH14 | ENST00000421213.1 | c.50-393G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000414155.1 |
Frequencies
GnomAD3 genomes AF: 0.485 AC: 73722AN: 152016Hom.: 18525 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
73722
AN:
152016
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.538 AC: 254AN: 472Hom.: 62 Cov.: 0 AF XY: 0.531 AC XY: 152AN XY: 286 show subpopulations
GnomAD4 exome
AF:
AC:
254
AN:
472
Hom.:
Cov.:
0
AF XY:
AC XY:
152
AN XY:
286
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
10
AN:
20
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
1
AN:
2
South Asian (SAS)
AF:
AC:
14
AN:
28
European-Finnish (FIN)
AF:
AC:
91
AN:
178
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
132
AN:
236
Other (OTH)
AF:
AC:
6
AN:
8
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
Heterozygous variant carriers
0
6
13
19
26
32
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.485 AC: 73753AN: 152134Hom.: 18524 Cov.: 34 AF XY: 0.482 AC XY: 35885AN XY: 74386 show subpopulations
GnomAD4 genome
AF:
AC:
73753
AN:
152134
Hom.:
Cov.:
34
AF XY:
AC XY:
35885
AN XY:
74386
show subpopulations
African (AFR)
AF:
AC:
14569
AN:
41480
American (AMR)
AF:
AC:
8061
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
1855
AN:
3470
East Asian (EAS)
AF:
AC:
2035
AN:
5176
South Asian (SAS)
AF:
AC:
2109
AN:
4824
European-Finnish (FIN)
AF:
AC:
5428
AN:
10580
Middle Eastern (MID)
AF:
AC:
167
AN:
294
European-Non Finnish (NFE)
AF:
AC:
37953
AN:
67978
Other (OTH)
AF:
AC:
1046
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1922
3843
5765
7686
9608
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1440
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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