Variant rs13045180 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001143967.2(EFCAB8):c.2893C>T(p.Gln965Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 416,780 control chromosomes in the GnomAD database, including 7,380 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. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.16 ( 2359 hom., cov: 32)

Exomes 𝑓: 0.18 ( 5021 hom. )

Consequence

EFCAB8
NM_001143967.2 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42

Variant links:

Genes affected

EFCAB8 (HGNC:34532): (EF-hand calcium binding domain 8) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

EFCAB8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB8	NM_001143967.2 linkuse as main transcript	c.2893C>T	p.Gln965Ter	stop_gained	23/27	ENST00000400522.9	NP_001137439.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB8	ENST00000400522.9 linkuse as main transcript	c.2893C>T	p.Gln965Ter	stop_gained	23/27	5	NM_001143967.2	ENSP00000383366	P1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23758

AN:

152080

Hom.:

2358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0479

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.184

AC:

48553

AN:

264582

Hom.:

5021

Cov.:

AF XY:

0.185

AC XY:

24679

AN XY:

133566

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.257

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.0134

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.195

Gnomad4 NFE exome

AF:

0.207

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.156

AC:

23769

AN:

152198

Hom.:

2359

Cov.:

AF XY:

0.159

AC XY:

11815

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0480

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.0205

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.183

Alfa

AF:

0.195

Hom.:

5752

Bravo

AF:

0.155

TwinsUK

AF:

0.209

AC:

774

ALSPAC

AF:

0.200

AC:

769

ESP6500AA

AF:

0.0470

AC:

ESP6500EA

AF:

0.217

AC:

692

Asia WGS

AF:

0.122

AC:

427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.36

CADD

Pathogenic

DANN

Benign

0.87

FATHMM_MKL

Benign

0.66

Vest4

0.25

GERP RS

4.4

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