Variant 16-88489056-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000319555.8(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
ENST00000319555.8 synonymous

Scores

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]

ZFPM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

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

Synonymous conserved (PhyloP=-0.967 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ZFPM1	NM_153813.3 linkuse as main transcript	c.171G>A	p.Pro57=	synonymous_variant	3/10	ENST00000319555.8	NP_722520.2
ZFPM1	XM_047433667.1 linkuse as main transcript	c.218G>A	p.Arg73His	missense_variant	3/9		XP_047289623.1
ZFPM1	XM_011522912.3 linkuse as main transcript	c.309G>A	p.Pro103=	synonymous_variant	3/10		XP_011521214.1
ZFPM1	XM_011522914.3 linkuse as main transcript	c.270G>A	p.Pro90=	synonymous_variant	3/10		XP_011521216.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM1	ENST00000319555.8 linkuse as main transcript	c.171G>A	p.Pro57=	synonymous_variant	3/10	1	NM_153813.3	ENSP00000326630	P1

Frequencies

GnomAD3 genomes

AF:

0.00116

AC:

176

AN:

152142

Hom.:

Cov.:

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.:

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.:

Cov.:

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

AF:

0.00115

AC:

175

AN:

152260

Hom.:

Cov.:

AF XY:

0.000967

AC XY:

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.:

Bravo

AF:

0.00132

Asia WGS

AF:

0.000577

AC:

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

ZFPM1: 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over