Variant chr19-39408027-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2

The ENST00000597629.3(ZFP36):c.309C>T(p.Arg103=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 1,613,562 control chromosomes in the GnomAD database, including 1,318 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 0.038 ( 116 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1202 hom. )

Consequence

ZFP36
ENST00000597629.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170

Variant links:

Genes affected

ZFP36 (HGNC:12862): (ZFP36 ring finger protein) Enables several functions, including 14-3-3 protein binding activity; heat shock protein binding activity; and mRNA 3'-UTR AU-rich region binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to growth factor stimulus; and regulation of gene expression. Acts upstream of or within mRNA catabolic process. Located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleus. Part of ribonucleoprotein complex. Colocalizes with RISC-loading complex. [provided by Alliance of Genome Resources, Apr 2022]

ZFP36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=0.17 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0377 (5741/152282) while in subpopulation NFE AF= 0.0405 (2751/68006). AF 95% confidence interval is 0.0392. There are 116 homozygotes in gnomad4. There are 2756 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 116 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP36	NM_003407.5 linkuse as main transcript	c.309C>T	p.Arg103=	synonymous_variant	2/2	ENST00000597629.3	NP_003398.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP36	ENST00000597629.3 linkuse as main transcript	c.309C>T	p.Arg103=	synonymous_variant	2/2	1	NM_003407.5	ENSP00000469647	P4

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5720

AN:

152164

Hom.:

111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0377

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0348

Gnomad ASJ

AF:

0.0504

Gnomad EAS

AF:

0.0379

Gnomad SAS

AF:

0.0333

Gnomad FIN

AF:

0.0193

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0404

Gnomad OTH

AF:

0.0468

GnomAD3 exomes

AF:

0.0351

AC:

8734

AN:

249002

Hom.:

180

AF XY:

0.0356

AC XY:

4807

AN XY:

135052

show subpopulations

Gnomad AFR exome

AF:

0.0374

Gnomad AMR exome

AF:

0.0229

Gnomad ASJ exome

AF:

0.0546

Gnomad EAS exome

AF:

0.0401

Gnomad SAS exome

AF:

0.0319

Gnomad FIN exome

AF:

0.0160

Gnomad NFE exome

AF:

0.0401

Gnomad OTH exome

AF:

0.0418

GnomAD4 exome

AF:

0.0399

AC:

58264

AN:

1461280

Hom.:

1202

Cov.:

AF XY:

0.0394

AC XY:

28661

AN XY:

727000

show subpopulations

Gnomad4 AFR exome

AF:

0.0406

Gnomad4 AMR exome

AF:

0.0251

Gnomad4 ASJ exome

AF:

0.0545

Gnomad4 EAS exome

AF:

0.0346

Gnomad4 SAS exome

AF:

0.0303

Gnomad4 FIN exome

AF:

0.0179

Gnomad4 NFE exome

AF:

0.0419

Gnomad4 OTH exome

AF:

0.0416

GnomAD4 genome

AF:

0.0377

AC:

5741

AN:

152282

Hom.:

116

Cov.:

AF XY:

0.0370

AC XY:

2756

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0382

Gnomad4 AMR

AF:

0.0347

Gnomad4 ASJ

AF:

0.0504

Gnomad4 EAS

AF:

0.0380

Gnomad4 SAS

AF:

0.0334

Gnomad4 FIN

AF:

0.0193

Gnomad4 NFE

AF:

0.0405

Gnomad4 OTH

AF:

0.0463

Alfa

AF:

0.0337

Hom.:

Bravo

AF:

0.0398

Asia WGS

AF:

0.0400

AC:

142

AN:

3478

EpiCase

AF:

0.0442

EpiControl

AF:

0.0464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

7.2

DANN

Benign

0.87

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over