Variant chr20-32885622-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001143967.2(EFCAB8):c.549G>A(p.Ser183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 1,551,758 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0093 ( 79 hom. )

Consequence

EFCAB8
NM_001143967.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.825

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 20-32885622-G-A is Benign according to our data. Variant chr20-32885622-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2652259.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.825 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB8	NM_001143967.2 linkuse as main transcript	c.549G>A	p.Ser183=	synonymous_variant	6/27	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.549G>A	p.Ser183=	synonymous_variant	6/27	5	NM_001143967.2	ENSP00000383366	P1

Frequencies

GnomAD3 genomes

AF:

0.00629

AC:

957

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00142

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00563

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.00603

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00764

GnomAD3 exomes

AF:

0.00648

AC:

1016

AN:

156872

Hom.:

AF XY:

0.00669

AC XY:

556

AN XY:

83088

show subpopulations

Gnomad AFR exome

AF:

0.000629

Gnomad AMR exome

AF:

0.00397

Gnomad ASJ exome

AF:

0.00259

Gnomad EAS exome

AF:

0.000183

Gnomad SAS exome

AF:

0.00799

Gnomad FIN exome

AF:

0.00564

Gnomad NFE exome

AF:

0.00949

Gnomad OTH exome

AF:

0.00794

GnomAD4 exome

AF:

0.00926

AC:

12953

AN:

1399484

Hom.:

Cov.:

AF XY:

0.00933

AC XY:

6437

AN XY:

690248

show subpopulations

Gnomad4 AFR exome

AF:

0.00177

Gnomad4 AMR exome

AF:

0.00417

Gnomad4 ASJ exome

AF:

0.00258

Gnomad4 EAS exome

AF:

0.0000560

Gnomad4 SAS exome

AF:

0.00806

Gnomad4 FIN exome

AF:

0.00588

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.00628

AC:

957

AN:

152274

Hom.:

Cov.:

AF XY:

0.00560

AC XY:

417

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00562

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00621

Gnomad4 FIN

AF:

0.00603

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00756

Alfa

AF:

0.00617

Hom.:

Bravo

AF:

0.00612

Asia WGS

AF:

0.00404

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

EFCAB8: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

1.3

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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