chr12-133048690-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001289971.2(ZNF84):​c.143-63A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,296,676 control chromosomes in the GnomAD database, including 123,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 16879 hom., cov: 32)
Exomes 𝑓: 0.43 ( 106166 hom. )

Consequence

ZNF84
NM_001289971.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.858
Variant links:
Genes affected
ZNF84 (HGNC:13159): (zinc finger protein 84) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 12-133048690-A-T is Benign according to our data. Variant chr12-133048690-A-T is described in ClinVar as [Benign]. Clinvar id is 982074.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF84NM_001289971.2 linkc.143-63A>T intron_variant Intron 3 of 4 ENST00000539354.6 NP_001276900.1 P51523

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF84ENST00000539354.6 linkc.143-63A>T intron_variant Intron 3 of 4 1 NM_001289971.2 ENSP00000445549.1 P51523

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69907
AN:
151844
Hom.:
16869
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.600
Gnomad AMI
AF:
0.433
Gnomad AMR
AF:
0.351
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.222
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.437
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.429
Gnomad OTH
AF:
0.404
GnomAD4 exome
AF:
0.426
AC:
487268
AN:
1144716
Hom.:
106166
Cov.:
14
AF XY:
0.427
AC XY:
247702
AN XY:
580166
show subpopulations
Gnomad4 AFR exome
AF:
0.603
Gnomad4 AMR exome
AF:
0.306
Gnomad4 ASJ exome
AF:
0.368
Gnomad4 EAS exome
AF:
0.223
Gnomad4 SAS exome
AF:
0.458
Gnomad4 FIN exome
AF:
0.425
Gnomad4 NFE exome
AF:
0.434
Gnomad4 OTH exome
AF:
0.419
GnomAD4 genome
AF:
0.460
AC:
69944
AN:
151960
Hom.:
16879
Cov.:
32
AF XY:
0.455
AC XY:
33823
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.600
Gnomad4 AMR
AF:
0.351
Gnomad4 ASJ
AF:
0.369
Gnomad4 EAS
AF:
0.223
Gnomad4 SAS
AF:
0.452
Gnomad4 FIN
AF:
0.437
Gnomad4 NFE
AF:
0.429
Gnomad4 OTH
AF:
0.401
Alfa
AF:
0.249
Hom.:
423
Bravo
AF:
0.454

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
-
Pathology and Clinical Laboratory Medicine, King Fahad Medical City
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.1
DANN
Benign
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs7314140; hg19: chr12-133625276; COSMIC: COSV59654452; COSMIC: COSV59654452; API