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GeneBe

2-218659583-G-A

Variant summary

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

The NM_001379659.1(ZNF142):c.-576C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152112 control chromosomes in the gnomAD Genomes database, including 336 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.056 ( 336 hom., cov: 32)

Consequence

ZNF142
NM_001379659.1 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.01

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 2-218659583-G-A is Benign according to our data. Variant chr2-218659583-G-A is described in ClinVar as [Benign]. Clinvar id is 1262585.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF142NM_001379659.1 linkuse as main transcriptc.-576C>T 5_prime_UTR_variant 1/11 ENST00000411696.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF142ENST00000411696.7 linkuse as main transcriptc.-576C>T 5_prime_UTR_variant 1/115 NM_001379659.1 P1

Frequencies

GnomAD3 genomes
AF:
0.0560
AC:
8515
AN:
152112
Hom.:
336
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.0312
Gnomad ASJ
AF:
0.0337
Gnomad EAS
AF:
0.117
Gnomad SAS
AF:
0.0437
Gnomad FIN
AF:
0.0271
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0339
Gnomad OTH
AF:
0.0507
GnomAD4 exome
AF:
0.0465
AC:
4
AN:
86
Hom.:
0
AF XY:
0.0690
AC XY:
4
AN XY:
58
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.167
Gnomad4 NFE exome
AF:
0.0286
Gnomad4 OTH exome
AF:
0.00
Alfa
AF:
0.0415
Hom.:
29
Bravo
AF:
0.0588
Asia WGS
AF:
0.0690
AC:
239
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxApr 02, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
9.6
Dann
Benign
0.75
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

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: rs28384379; hg19: chr2-219524306; API