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GeneBe

rs964184

Variant summary

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

The NM_003904.5(ZPR1):c.*724C>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 0.823 in 152,238 control chromosomes in the GnomAD database, including 51,799 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 0.82 ( 51773 hom., cov: 32)
Exomes 𝑓: 0.88 ( 26 hom. )

Consequence

ZPR1
NM_003904.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.346
Variant links:
Genes affected
ZPR1 (HGNC:13051): (ZPR1 zinc finger) The protein encoded by this gene is found in the cytoplasm of quiescent cells but translocates to the nucleolus in proliferating cells. The encoded protein interacts with survival motor neuron protein (SMN1) to enhance pre-mRNA splicing and to induce neuronal differentiation and axonal growth. Defects in this gene or the SMN1 gene can cause spinal muscular atrophy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZPR1NM_003904.5 linkuse as main transcriptc.*724C>G 3_prime_UTR_variant 14/14 ENST00000227322.8
ZPR1NM_001317086.2 linkuse as main transcriptc.*724C>G 3_prime_UTR_variant 13/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZPR1ENST00000227322.8 linkuse as main transcriptc.*724C>G 3_prime_UTR_variant 14/141 NM_003904.5 P1
ZPR1ENST00000429220.5 linkuse as main transcriptc.*724C>G 3_prime_UTR_variant 12/125
ZPR1ENST00000444935.5 linkuse as main transcriptc.*724C>G 3_prime_UTR_variant 13/135

Frequencies

GnomAD3 genomes
AF:
0.823
AC:
125152
AN:
152052
Hom.:
51754
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.791
Gnomad AMI
AF:
0.773
Gnomad AMR
AF:
0.752
Gnomad ASJ
AF:
0.824
Gnomad EAS
AF:
0.768
Gnomad SAS
AF:
0.766
Gnomad FIN
AF:
0.863
Gnomad MID
AF:
0.756
Gnomad NFE
AF:
0.862
Gnomad OTH
AF:
0.808
GnomAD4 exome
AF:
0.882
AC:
60
AN:
68
Hom.:
26
Cov.:
0
AF XY:
0.909
AC XY:
40
AN XY:
44
show subpopulations
Gnomad4 AFR exome
AF:
1.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.833
Gnomad4 NFE exome
AF:
0.870
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.823
AC:
125222
AN:
152170
Hom.:
51773
Cov.:
32
AF XY:
0.821
AC XY:
61051
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.791
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.824
Gnomad4 EAS
AF:
0.767
Gnomad4 SAS
AF:
0.765
Gnomad4 FIN
AF:
0.863
Gnomad4 NFE
AF:
0.862
Gnomad4 OTH
AF:
0.804
Alfa
AF:
0.852
Hom.:
30562
Bravo
AF:
0.813
Asia WGS
AF:
0.765
AC:
2662
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.48
Dann
Benign
0.42

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: rs964184; hg19: chr11-116648917; API