Variant chr17-47361422-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The ENST00000331493.7(EFCAB13):c.706C>T(p.Arg236Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00952 in 1,613,472 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0077 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0097 ( 84 hom. )

Consequence

EFCAB13
ENST00000331493.7 stop_gained

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.50

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 Likely_benign. Variant got -5 ACMG points.

BP6

Variant 17-47361422-C-T is Benign according to our data. Variant chr17-47361422-C-T is described in ClinVar as [Benign]. Clinvar id is 3041441.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB13	NM_152347.5 linkuse as main transcript	c.706C>T	p.Arg236Ter	stop_gained	10/25	ENST00000331493.7	NP_689560.3
EFCAB13	NM_001195192.2 linkuse as main transcript	c.518-9015C>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.706C>T	p.Arg236Ter	stop_gained	10/25	1	NM_152347.5	ENSP00000332111	A2	Q8IY85-1
EFCAB13	ENST00000517310.5 linkuse as main transcript	c.74-9015C>T		intron_variant		2		ENSP00000466136
EFCAB13	ENST00000517484.5 linkuse as main transcript	c.518-9015C>T		intron_variant		2		ENSP00000430048	P2	Q8IY85-2
EFCAB13	ENST00000520776.5 linkuse as main transcript	n.696C>T		non_coding_transcript_exon_variant	7/14	2

Frequencies

GnomAD3 genomes

AF:

0.00774

AC:

1177

AN:

151976

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00191

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.0125

Gnomad ASJ

AF:

0.0147

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00625

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.0106

Gnomad OTH

AF:

0.0206

GnomAD3 exomes

AF:

0.00791

AC:

1987

AN:

251326

Hom.:

AF XY:

0.00837

AC XY:

1137

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.00178

Gnomad AMR exome

AF:

0.00813

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.000598

Gnomad SAS exome

AF:

0.00114

Gnomad FIN exome

AF:

0.00615

Gnomad NFE exome

AF:

0.0114

Gnomad OTH exome

AF:

0.00766

GnomAD4 exome

AF:

0.00970

AC:

14178

AN:

1461378

Hom.:

Cov.:

AF XY:

0.00958

AC XY:

6961

AN XY:

726988

show subpopulations

Gnomad4 AFR exome

AF:

0.00179

Gnomad4 AMR exome

AF:

0.00834

Gnomad4 ASJ exome

AF:

0.0136

Gnomad4 EAS exome

AF:

0.000278

Gnomad4 SAS exome

AF:

0.00122

Gnomad4 FIN exome

AF:

0.00588

Gnomad4 NFE exome

AF:

0.0111

Gnomad4 OTH exome

AF:

0.00883

GnomAD4 genome

AF:

0.00775

AC:

1178

AN:

152094

Hom.:

Cov.:

AF XY:

0.00738

AC XY:

549

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.00190

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.0147

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00625

Gnomad4 NFE

AF:

0.0106

Gnomad4 OTH

AF:

0.0204

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.00830

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.0122

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.00988

AC:

ExAC

AF:

0.00772

AC:

937

Asia WGS

AF:

0.00173

AC:

AN:

3478

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 20, 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

Pathogenic

0.18

BayesDel_noAF

Pathogenic

0.50

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Benign

0.18

Eigen_PC

Benign

-0.069

FATHMM_MKL

Benign

0.46

MutationTaster

Benign

1.0

A;D

Vest4

0.15

GERP RS

1.7

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