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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(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 152052 control chromosomes in the gnomAD Genomes database, including 51754 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 ( 51754 hom., cov: 32)

Consequence

ZPR1
NM_003904 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.346

Links

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
?
GnomAd 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
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
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
0.43
Dann
Benign
0.42

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: rs964184; hg19: chr11-116648917;