rs4679372

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021964.3(ZNF148):​c.*2633C>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 0.776 in 152,028 control chromosomes in the GnomAD database, including 46,437 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 0.78 ( 46437 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

ZNF148
NM_021964.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0380
Variant links:
Genes affected
ZNF148 (HGNC:12933): (zinc finger protein 148) The protein encoded by this gene is a member of the Kruppel family of zinc finger DNA binding proteins. The encoded protein activates transcription of the T-cell receptor and intestinal alkaline phosphatase genes but represses transcription of the ornithine decarboxylase, vimentin, gastrin, stomelysin, and enolase genes. Increased expression of this gene results in decreased patient survival rates from colorectal cancer, while mutations in this gene have been associated with global developmental delay, hypoplastic corpus callosum, and dysmorphic facies. [provided by RefSeq, Feb 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF148NM_021964.3 linkuse as main transcriptc.*2633C>T 3_prime_UTR_variant 9/9 ENST00000360647.9 NP_068799.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF148ENST00000360647.9 linkuse as main transcriptc.*2633C>T 3_prime_UTR_variant 9/91 NM_021964.3 ENSP00000353863 P1Q9UQR1-1

Frequencies

GnomAD3 genomes
AF:
0.776
AC:
117951
AN:
151910
Hom.:
46408
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.872
Gnomad AMI
AF:
0.817
Gnomad AMR
AF:
0.691
Gnomad ASJ
AF:
0.826
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.666
Gnomad FIN
AF:
0.770
Gnomad MID
AF:
0.829
Gnomad NFE
AF:
0.764
Gnomad OTH
AF:
0.784
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.776
AC:
118034
AN:
152028
Hom.:
46437
Cov.:
31
AF XY:
0.772
AC XY:
57362
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.871
Gnomad4 AMR
AF:
0.690
Gnomad4 ASJ
AF:
0.826
Gnomad4 EAS
AF:
0.502
Gnomad4 SAS
AF:
0.665
Gnomad4 FIN
AF:
0.770
Gnomad4 NFE
AF:
0.764
Gnomad4 OTH
AF:
0.784
Alfa
AF:
0.765
Hom.:
42176
Bravo
AF:
0.771
Asia WGS
AF:
0.631
AC:
2195
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.60
DANN
Benign
0.57

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: rs4679372; hg19: chr3-124948552; API