Variant 14-88620934-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_183387.3(EML5):c.5203-9_5203-8insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 22455 hom., cov: 0)

Exomes 𝑓: 0.32 ( 71 hom. )

Failed GnomAD Quality Control

Consequence

EML5
NM_183387.3 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.252

Variant links:

Genes affected

ZC3H14 (HGNC:20509): (zinc finger CCCH-type containing 14) The protein encoded by this gene is a poly(A)-binding protein that can affect gene expression and poly(A) tail length. The encoded protein may influence mRNA stability, nuclear export, and translation. [provided by RefSeq, May 2016]

ZC3H14 links:

EML5 (HGNC:18197): (EMAP like 5) Predicted to enable microtubule binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

EML5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 14-88620934-T-TA is Benign according to our data. Variant chr14-88620934-T-TA is described in ClinVar as [Benign]. Clinvar id is 402826.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H14	NM_024824.5 linkuse as main transcript	c.*9200dup		3_prime_UTR_variant	17/17	ENST00000251038.10
EML5	NM_183387.3 linkuse as main transcript	c.5203-9_5203-8insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000554922.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H14	ENST00000251038.10 linkuse as main transcript	c.*9200dup		3_prime_UTR_variant	17/17	1	NM_024824.5	P3	Q6PJT7-1
EML5	ENST00000554922.6 linkuse as main transcript	c.5203-9_5203-8insT		splice_polypyrimidine_tract_variant, intron_variant		5	NM_183387.3	P4	Q05BV3-5

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

78593

AN:

138858

Hom.:

22462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.687

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.625

Gnomad MID

AF:

0.697

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.632

GnomAD3 exomes

AF:

0.250

AC:

13083

AN:

52316

Hom.:

AF XY:

0.245

AC XY:

6446

AN XY:

26334

show subpopulations

Gnomad AFR exome

AF:

0.195

Gnomad AMR exome

AF:

0.308

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.223

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.260

Gnomad OTH exome

AF:

0.280

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.322

AC:

392122

AN:

1218028

Hom.:

Cov.:

AF XY:

0.319

AC XY:

189271

AN XY:

593774

show subpopulations

Gnomad4 AFR exome

AF:

0.231

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.330

Gnomad4 EAS exome

AF:

0.236

Gnomad4 SAS exome

AF:

0.236

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.566

AC:

78572

AN:

138864

Hom.:

22455

Cov.:

AF XY:

0.568

AC XY:

37881

AN XY:

66710

show subpopulations

Gnomad4 AFR

AF:

0.429

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.687

Gnomad4 EAS

AF:

0.491

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.625

Gnomad4 NFE

AF:

0.620

Gnomad4 OTH

AF:

0.635

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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