rs10749863

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014774.3(EFCAB14):​c.335-605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,250 control chromosomes in the GnomAD database, including 49,469 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 0.80 ( 49469 hom., cov: 33)

Consequence

EFCAB14
NM_014774.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

7 publications found
Variant links:
Genes affected
EFCAB14 (HGNC:29051): (EF-hand calcium binding domain 14) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EFCAB14NM_014774.3 linkc.335-605C>T intron_variant Intron 2 of 10 ENST00000371933.8 NP_055589.1 O75071

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EFCAB14ENST00000371933.8 linkc.335-605C>T intron_variant Intron 2 of 10 1 NM_014774.3 ENSP00000361001.3 O75071

Frequencies

GnomAD3 genomes
AF:
0.805
AC:
122402
AN:
152132
Hom.:
49397
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.837
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.868
Gnomad ASJ
AF:
0.779
Gnomad EAS
AF:
0.912
Gnomad SAS
AF:
0.729
Gnomad FIN
AF:
0.777
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.774
Gnomad OTH
AF:
0.825
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.805
AC:
122530
AN:
152250
Hom.:
49469
Cov.:
33
AF XY:
0.807
AC XY:
60100
AN XY:
74436
show subpopulations
African (AFR)
AF:
0.838
AC:
34797
AN:
41542
American (AMR)
AF:
0.868
AC:
13275
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.779
AC:
2704
AN:
3472
East Asian (EAS)
AF:
0.912
AC:
4735
AN:
5190
South Asian (SAS)
AF:
0.729
AC:
3518
AN:
4828
European-Finnish (FIN)
AF:
0.777
AC:
8219
AN:
10584
Middle Eastern (MID)
AF:
0.867
AC:
255
AN:
294
European-Non Finnish (NFE)
AF:
0.774
AC:
52611
AN:
68014
Other (OTH)
AF:
0.828
AC:
1751
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1244
2489
3733
4978
6222
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
876
1752
2628
3504
4380
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.793
Hom.:
19325
Bravo
AF:
0.814
Asia WGS
AF:
0.821
AC:
2855
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.5
DANN
Benign
0.77
PhyloP100
-0.040
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs10749863; hg19: chr1-47174328; API