rs2288421

Variant summary

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

The NM_001322131.2(ZNF160):​c.*24A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,565,046 control chromosomes in the GnomAD database, including 62,914 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 0.23 ( 5007 hom., cov: 32)
Exomes 𝑓: 0.28 ( 57907 hom. )

Consequence

ZNF160
NM_001322131.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74
Variant links:
Genes affected
ZNF160 (HGNC:12948): (zinc finger protein 160) The protein encoded by this gene is a Kruppel-related zinc finger protein which is characterized by the presence of an N-terminal repressor domain, the Kruppel-associated box (KRAB). The KRAB domain is a potent repressor of transcription; thus this protein may function in transcription regulation. Multiple transcript variants have been found for this gene. [provided by RefSeq, Apr 2016]

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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF160NM_001322131.2 linkuse as main transcriptc.*24A>G 3_prime_UTR_variant 6/6 ENST00000683776.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF160ENST00000683776.1 linkuse as main transcriptc.*24A>G 3_prime_UTR_variant 6/6 NM_001322131.2 P1Q9HCG1-1

Frequencies

GnomAD3 genomes
AF:
0.231
AC:
35159
AN:
151994
Hom.:
4999
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0772
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.292
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.307
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.235
GnomAD3 exomes
AF:
0.268
AC:
57486
AN:
214510
Hom.:
8554
AF XY:
0.265
AC XY:
30123
AN XY:
113850
show subpopulations
Gnomad AFR exome
AF:
0.0671
Gnomad AMR exome
AF:
0.358
Gnomad ASJ exome
AF:
0.266
Gnomad EAS exome
AF:
0.300
Gnomad SAS exome
AF:
0.126
Gnomad FIN exome
AF:
0.296
Gnomad NFE exome
AF:
0.292
Gnomad OTH exome
AF:
0.281
GnomAD4 exome
AF:
0.281
AC:
397208
AN:
1412934
Hom.:
57907
Cov.:
32
AF XY:
0.276
AC XY:
192709
AN XY:
697362
show subpopulations
Gnomad4 AFR exome
AF:
0.0653
Gnomad4 AMR exome
AF:
0.353
Gnomad4 ASJ exome
AF:
0.268
Gnomad4 EAS exome
AF:
0.328
Gnomad4 SAS exome
AF:
0.128
Gnomad4 FIN exome
AF:
0.295
Gnomad4 NFE exome
AF:
0.294
Gnomad4 OTH exome
AF:
0.269
GnomAD4 genome
AF:
0.231
AC:
35176
AN:
152112
Hom.:
5007
Cov.:
32
AF XY:
0.234
AC XY:
17394
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0770
Gnomad4 AMR
AF:
0.354
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.292
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.307
Gnomad4 NFE
AF:
0.284
Gnomad4 OTH
AF:
0.234
Alfa
AF:
0.274
Hom.:
8480
Bravo
AF:
0.231
Asia WGS
AF:
0.194
AC:
676
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.5
DANN
Benign
0.60

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: rs2288421; hg19: chr19-53571306; COSMIC: COSV105268163; COSMIC: COSV105268163; API