Variant rs8123073 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001143967.2(EFCAB8):c.-11+46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 470,962 control chromosomes in the GnomAD database, including 780 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 0.058 ( 533 hom., cov: 32)

Exomes 𝑓: 0.026 ( 247 hom. )

Consequence

EFCAB8
NM_001143967.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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.-11+46A>G		intron_variant		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.-11+46A>G		intron_variant		5	NM_001143967.2	ENSP00000383366	P1

Frequencies

GnomAD3 genomes

AF:

0.0580

AC:

8819

AN:

152098

Hom.:

532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0235

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0449

Gnomad FIN

AF:

0.0166

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0193

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0258

AC:

3904

AN:

151140

Hom.:

141

AF XY:

0.0257

AC XY:

2087

AN XY:

81170

show subpopulations

Gnomad AFR exome

AF:

0.164

Gnomad AMR exome

AF:

0.0126

Gnomad ASJ exome

AF:

0.00203

Gnomad EAS exome

AF:

0.00223

Gnomad SAS exome

AF:

0.0436

Gnomad FIN exome

AF:

0.0162

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0167

GnomAD4 exome

AF:

0.0261

AC:

8320

AN:

318746

Hom.:

247

Cov.:

AF XY:

0.0262

AC XY:

4715

AN XY:

180064

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.0125

Gnomad4 ASJ exome

AF:

0.00297

Gnomad4 EAS exome

AF:

0.00206

Gnomad4 SAS exome

AF:

0.0399

Gnomad4 FIN exome

AF:

0.0160

Gnomad4 NFE exome

AF:

0.0211

Gnomad4 OTH exome

AF:

0.0256

GnomAD4 genome

AF:

0.0580

AC:

8833

AN:

152216

Hom.:

533

Cov.:

AF XY:

0.0575

AC XY:

4277

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.0233

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.0442

Gnomad4 FIN

AF:

0.0166

Gnomad4 NFE

AF:

0.0193

Gnomad4 OTH

AF:

0.0322

Alfa

AF:

0.0255

Hom.:

Bravo

AF:

0.0617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

DANN

Benign

0.72

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