15-42435462-C-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001366845.3(ZNF106):ā€‹c.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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.76
Variant links:
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
ZNF106NM_001366845.3 linkuse as main transcriptc.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
ZNF106ENST00000564754.7 linkuse as main transcriptc.4803G>C p.Leu1601= synonymous_variant 14/221 NM_001366845.3 ENSP00000456845 P1

Frequencies

GnomAD3 genomes
AF:
0.00271
AC:
412
AN:
152136
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000893
Gnomad AMI
AF:
0.00330
Gnomad AMR
AF:
0.00183
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00349
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00431
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.00321
AC:
806
AN:
251476
Hom.:
3
AF XY:
0.00324
AC XY:
441
AN XY:
135910
show subpopulations
Gnomad AFR exome
AF:
0.000923
Gnomad AMR exome
AF:
0.00332
Gnomad ASJ exome
AF:
0.00238
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00101
Gnomad FIN exome
AF:
0.00342
Gnomad NFE exome
AF:
0.00457
Gnomad OTH exome
AF:
0.00440
GnomAD4 exome
AF:
0.00405
AC:
5916
AN:
1461888
Hom.:
14
Cov.:
31
AF XY:
0.00394
AC XY:
2864
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.000806
Gnomad4 AMR exome
AF:
0.00306
Gnomad4 ASJ exome
AF:
0.00187
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00108
Gnomad4 FIN exome
AF:
0.00335
Gnomad4 NFE exome
AF:
0.00471
Gnomad4 OTH exome
AF:
0.00308
GnomAD4 genome
AF:
0.00271
AC:
412
AN:
152254
Hom.:
2
Cov.:
32
AF XY:
0.00286
AC XY:
213
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000891
Gnomad4 AMR
AF:
0.00183
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00349
Gnomad4 NFE
AF:
0.00431
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00361
Hom.:
1
Bravo
AF:
0.00264
Asia WGS
AF:
0.000577
AC:
3
AN:
3478
EpiCase
AF:
0.00344
EpiControl
AF:
0.00409

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenSep 01, 2022ZNF106: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
CADD
Benign
15
DANN
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.31
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.31
Position offset: -10

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs141371905; hg19: chr15-42727660; API