dbSNP rs78561706: EFCAB13:p.Lys113Lys (chr17-47344197-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_152347.5(EFCAB13):c.339G>A(p.Lys113Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00611 in 1,613,128 control chromosomes in the GnomAD database, including 255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.013 ( 35 hom., cov: 32)

Exomes 𝑓: 0.0054 ( 220 hom. )

Consequence

EFCAB13
NM_152347.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.38

Variant links:

Genes affected

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

EFCAB13 links:

ENSG00000259753 (HGNC:):

ENSG00000259753 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 17-47344197-G-A is Benign according to our data. Variant chr17-47344197-G-A is described in ClinVar as [Benign]. Clinvar id is 3039578.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=3.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB13	NM_152347.5 link	c.339G>A	p.Lys113Lys	synonymous_variant	Exon 7 of 25	ENST00000331493.7	NP_689560.3	Q8IY85-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
EFCAB13	ENST00000331493.7 link	c.339G>A	p.Lys113Lys	synonymous_variant	Exon 7 of 25	1	NM_152347.5	ENSP00000332111.2	Q8IY85-1
ENSG00000259753	ENST00000560629.1 link	n.*328G>A		non_coding_transcript_exon_variant	Exon 18 of 18	2		ENSP00000456711.2	H3BM21
ENSG00000259753	ENST00000560629.1 link	n.*328G>A		3_prime_UTR_variant	Exon 18 of 18	2		ENSP00000456711.2	H3BM21

Frequencies

GnomAD3 genomes

AF:

0.0126

AC:

1922

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0298

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00524

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0649

Gnomad SAS

AF:

0.0418

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000603

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0124

AC:

3109

AN:

250986

Hom.:

104

AF XY:

0.0131

AC XY:

1772

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.0300

Gnomad AMR exome

AF:

0.00238

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0704

Gnomad SAS exome

AF:

0.0381

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000458

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00543

AC:

7928

AN:

1460916

Hom.:

220

Cov.:

AF XY:

0.00646

AC XY:

4693

AN XY:

726762

show subpopulations

Gnomad4 AFR exome

AF:

0.0323

Gnomad4 AMR exome

AF:

0.00253

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0603

Gnomad4 SAS exome

AF:

0.0386

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000328

Gnomad4 OTH exome

AF:

0.00982

GnomAD4 genome

AF:

0.0127

AC:

1936

AN:

152212

Hom.:

Cov.:

AF XY:

0.0135

AC XY:

1001

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0300

Gnomad4 AMR

AF:

0.00523

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0649

Gnomad4 SAS

AF:

0.0421

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000603

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.00542

Hom.:

Bravo

AF:

0.0135

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

EpiCase

AF:

0.000819

EpiControl

AF:

0.000593

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EFCAB13-related disorder

Benign:1

Feb 19, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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_noAF

Benign

-0.49

CADD

Benign

8.6

DANN

Benign

0.77

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