Variant chr17-47347921-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_152347.5(EFCAB13):c.631C>T(p.Arg211Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,529,114 control chromosomes in the GnomAD database, including 3,898 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.052 ( 389 hom., cov: 30)

Exomes 𝑓: 0.061 ( 3509 hom. )

Consequence

EFCAB13
NM_152347.5 stop_gained

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

EFCAB13 (HGNC:26864): (EF-hand calcium binding domain 13)

EFCAB13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 17-47347921-C-T is Benign according to our data. Variant chr17-47347921-C-T is described in ClinVar as [Benign]. Clinvar id is 3059359.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB13	NM_152347.5 linkuse as main transcript	c.631C>T	p.Arg211Ter	stop_gained	9/25	ENST00000331493.7	NP_689560.3
EFCAB13	NM_001195192.2 linkuse as main transcript	c.517+2823C>T		intron_variant			NP_001182121.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB13	ENST00000331493.7 linkuse as main transcript	c.631C>T	p.Arg211Ter	stop_gained	9/25	1	NM_152347.5	ENSP00000332111	A2	Q8IY85-1
EFCAB13	ENST00000517310.5 linkuse as main transcript	c.73+2823C>T		intron_variant		2		ENSP00000466136
EFCAB13	ENST00000517484.5 linkuse as main transcript	c.517+2823C>T		intron_variant		2		ENSP00000430048	P2	Q8IY85-2
EFCAB13	ENST00000520776.5 linkuse as main transcript	n.651+2823C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0520

AC:

7896

AN:

151978

Hom.:

389

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0361

Gnomad ASJ

AF:

0.0363

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0524

Gnomad OTH

AF:

0.0569

GnomAD3 exomes

AF:

0.0737

AC:

17721

AN:

240478

Hom.:

1074

AF XY:

0.0763

AC XY:

9935

AN XY:

130130

show subpopulations

Gnomad AFR exome

AF:

0.00901

Gnomad AMR exome

AF:

0.0227

Gnomad ASJ exome

AF:

0.0392

Gnomad EAS exome

AF:

0.241

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0564

Gnomad OTH exome

AF:

0.0677

GnomAD4 exome

AF:

0.0609

AC:

83832

AN:

1377018

Hom.:

3509

Cov.:

AF XY:

0.0623

AC XY:

42140

AN XY:

676276

show subpopulations

Gnomad4 AFR exome

AF:

0.00934

Gnomad4 AMR exome

AF:

0.0245

Gnomad4 ASJ exome

AF:

0.0398

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.0522

Gnomad4 OTH exome

AF:

0.0699

GnomAD4 genome

AF:

0.0518

AC:

7884

AN:

152096

Hom.:

389

Cov.:

AF XY:

0.0558

AC XY:

4146

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0109

Gnomad4 AMR

AF:

0.0361

Gnomad4 ASJ

AF:

0.0363

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.0524

Gnomad4 OTH

AF:

0.0568

Alfa

AF:

0.0548

Hom.:

376

Bravo

AF:

0.0436

TwinsUK

AF:

0.0475

AC:

176

ALSPAC

AF:

0.0462

AC:

178

ESP6500AA

AF:

0.0134

AC:

ESP6500EA

AF:

0.0533

AC:

458

ExAC

AF:

0.0734

AC:

8913

Asia WGS

AF:

0.188

AC:

651

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EFCAB13-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 19, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.042

BayesDel_noAF

Pathogenic

0.31

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.24

FATHMM_MKL

Benign

0.26

MutationTaster

Benign

8.3e-16

P;P

Vest4

0.075

GERP RS

2.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.56

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.56

Position offset: 30

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