15-42435462-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001366845.3(ZNF106):āc.4803G>Cā(p.Leu1601=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00392 in 1,614,142 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0027 ( 2 hom., cov: 32)
Exomes š: 0.0040 ( 14 hom. )
Consequence
ZNF106
NM_001366845.3 synonymous
NM_001366845.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.76
Genes affected
ZNF106 (HGNC:12886): (zinc finger protein 106) Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 15-42435462-C-G is Benign according to our data. Variant chr15-42435462-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2645238.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF106 | NM_001366845.3 | c.4803G>C | p.Leu1601= | synonymous_variant | 14/22 | ENST00000564754.7 | NP_001353774.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF106 | ENST00000564754.7 | c.4803G>C | p.Leu1601= | synonymous_variant | 14/22 | 1 | NM_001366845.3 | ENSP00000456845 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00271 AC: 412AN: 152136Hom.: 2 Cov.: 32
GnomAD3 genomes
AF:
AC:
412
AN:
152136
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.00321 AC: 806AN: 251476Hom.: 3 AF XY: 0.00324 AC XY: 441AN XY: 135910
GnomAD3 exomes
AF:
AC:
806
AN:
251476
Hom.:
AF XY:
AC XY:
441
AN XY:
135910
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00405 AC: 5916AN: 1461888Hom.: 14 Cov.: 31 AF XY: 0.00394 AC XY: 2864AN XY: 727244
GnomAD4 exome
AF:
AC:
5916
AN:
1461888
Hom.:
Cov.:
31
AF XY:
AC XY:
2864
AN XY:
727244
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00271 AC: 412AN: 152254Hom.: 2 Cov.: 32 AF XY: 0.00286 AC XY: 213AN XY: 74450
GnomAD4 genome
AF:
AC:
412
AN:
152254
Hom.:
Cov.:
32
AF XY:
AC XY:
213
AN XY:
74450
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | ZNF106: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -10
Find out detailed SpliceAI scores and Pangolin per-transcript scores at