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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.346

Links

ZPR1 (HGNC:13051):

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
ZPR1	NM_003904.5 linkuse as main transcript	c.*724C>G		3_prime_UTR_variant	14/14	ENST00000227322.8
ZPR1	NM_001317086.2 linkuse as main transcript	c.*724C>G		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
ZPR1	ENST00000227322.8 linkuse as main transcript	c.*724C>G	3_prime_UTR_variant	14/14	1	NM_003904.5	P1
ZPR1	ENST00000429220.5 linkuse as main transcript	c.*724C>G	3_prime_UTR_variant	12/12	5
ZPR1	ENST00000444935.5 linkuse as main transcript	c.*724C>G	3_prime_UTR_variant	13/13	5

Frequencies

GnomAD3 genomes

AF:

0.823

AC:

125152

AN:

152052

Hom.:

51754

Cov.:

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:

AN:

Hom.:

AF XY:

0.909

AC XY:

AN XY:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over