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GeneBe

16-88489056-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_153813.3(ZFPM1):c.171G>A(p.Pro57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,612,736 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0015 ( 5 hom. )

Consequence

ZFPM1
NM_153813.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.967
Variant links:
Genes affected
ZFPM1 (HGNC:19762): (zinc finger protein, FOG family member 1) Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and transcription corepressor activity. Involved in platelet formation; regulation of definitive erythrocyte differentiation; and regulation of gene expression. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-88489056-G-A is Benign according to our data. Variant chr16-88489056-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646973.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.967 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZFPM1NM_153813.3 linkuse as main transcriptc.171G>A p.Pro57= synonymous_variant 3/10 ENST00000319555.8
ZFPM1XM_047433667.1 linkuse as main transcriptc.218G>A p.Arg73His missense_variant 3/9
ZFPM1XM_011522912.3 linkuse as main transcriptc.309G>A p.Pro103= synonymous_variant 3/10
ZFPM1XM_011522914.3 linkuse as main transcriptc.270G>A p.Pro90= synonymous_variant 3/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZFPM1ENST00000319555.8 linkuse as main transcriptc.171G>A p.Pro57= synonymous_variant 3/101 NM_153813.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00116
AC:
176
AN:
152142
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000435
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00170
Gnomad ASJ
AF:
0.00491
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00157
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00133
AC:
331
AN:
248668
Hom.:
0
AF XY:
0.00136
AC XY:
184
AN XY:
134938
show subpopulations
Gnomad AFR exome
AF:
0.000187
Gnomad AMR exome
AF:
0.00180
Gnomad ASJ exome
AF:
0.00413
Gnomad EAS exome
AF:
0.0000547
Gnomad SAS exome
AF:
0.000753
Gnomad FIN exome
AF:
0.0000465
Gnomad NFE exome
AF:
0.00169
Gnomad OTH exome
AF:
0.00182
GnomAD4 exome
AF:
0.00150
AC:
2188
AN:
1460476
Hom.:
5
Cov.:
31
AF XY:
0.00155
AC XY:
1126
AN XY:
726534
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.00168
Gnomad4 ASJ exome
AF:
0.00537
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.000638
Gnomad4 FIN exome
AF:
0.0000759
Gnomad4 NFE exome
AF:
0.00161
Gnomad4 OTH exome
AF:
0.00147
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00115
AC:
175
AN:
152260
Hom.:
0
Cov.:
34
AF XY:
0.000967
AC XY:
72
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.00170
Gnomad4 ASJ
AF:
0.00491
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00156
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00173
Hom.:
0
Bravo
AF:
0.00132
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00224
EpiControl
AF:
0.00273

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenDec 01, 2022ZFPM1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
2.5
Dann
Benign
0.58
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
3.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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: rs148828760; hg19: chr16-88555464; API