rs179320

Variant summary

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

The NM_018260.3(ZNF701):​c.*1723A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,238 control chromosomes in the GnomAD database, including 37,484 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 0.70 ( 37441 hom., cov: 32)
Exomes 𝑓: 0.76 ( 43 hom. )

Consequence

ZNF701
NM_018260.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26
Variant links:
Genes affected
ZNF701 (HGNC:25597): (zinc finger protein 701) 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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF701NM_018260.3 linkuse as main transcriptc.*1723A>C 3_prime_UTR_variant 4/4 ENST00000391785.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF701ENST00000391785.8 linkuse as main transcriptc.*1723A>C 3_prime_UTR_variant 4/41 NM_018260.3 P2Q9NV72-2
ZNF701ENST00000540331.1 linkuse as main transcriptc.*1723A>C 3_prime_UTR_variant 5/51 A2Q9NV72-1
ENST00000599222.1 linkuse as main transcriptn.382T>G non_coding_transcript_exon_variant 1/23

Frequencies

GnomAD3 genomes
AF:
0.699
AC:
106194
AN:
151976
Hom.:
37390
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.673
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.639
Gnomad ASJ
AF:
0.705
Gnomad EAS
AF:
0.505
Gnomad SAS
AF:
0.717
Gnomad FIN
AF:
0.697
Gnomad MID
AF:
0.731
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.703
GnomAD4 exome
AF:
0.757
AC:
109
AN:
144
Hom.:
43
Cov.:
0
AF XY:
0.804
AC XY:
90
AN XY:
112
show subpopulations
Gnomad4 AFR exome
AF:
0.600
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.746
Gnomad4 OTH exome
AF:
0.875
GnomAD4 genome
AF:
0.699
AC:
106309
AN:
152094
Hom.:
37441
Cov.:
32
AF XY:
0.695
AC XY:
51715
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.674
Gnomad4 AMR
AF:
0.639
Gnomad4 ASJ
AF:
0.705
Gnomad4 EAS
AF:
0.506
Gnomad4 SAS
AF:
0.717
Gnomad4 FIN
AF:
0.697
Gnomad4 NFE
AF:
0.738
Gnomad4 OTH
AF:
0.708
Alfa
AF:
0.688
Hom.:
4580
Bravo
AF:
0.694
Asia WGS
AF:
0.636
AC:
2214
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.74
DANN
Benign
0.62

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: rs179320; hg19: chr19-53088433; API