GeneBe

NM_198529.4:c.2365+535A>G

Variant names:

Variant summary

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

The NM_198529.4(EFCAB5):​c.2365+535A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,212 control chromosomes in the GnomAD database, including 2,827 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 0.17 ( 2827 hom., cov: 32)

Consequence

EFCAB5
NM_198529.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.398

Publications

9 publications found
Variant links:
Genes affected
EFCAB5 (HGNC:24801): (EF-hand calcium binding domain 5) Predicted to enable calcium ion binding activity. [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=-0.66).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EFCAB5NM_198529.4 linkc.2365+535A>G intron_variant Intron 12 of 22 ENST00000394835.8 NP_940931.3 A4FU69-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EFCAB5ENST00000394835.8 linkc.2365+535A>G intron_variant Intron 12 of 22 1 NM_198529.4 ENSP00000378312.3 A4FU69-1

Frequencies

GnomAD3 genomes
AF:
0.168
AC:
25486
AN:
152094
Hom.:
2824
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0478
Gnomad AMI
AF:
0.278
Gnomad AMR
AF:
0.161
Gnomad ASJ
AF:
0.197
Gnomad EAS
AF:
0.0298
Gnomad SAS
AF:
0.112
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.242
Gnomad OTH
AF:
0.169
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.167
AC:
25489
AN:
152212
Hom.:
2827
Cov.:
32
AF XY:
0.162
AC XY:
12091
AN XY:
74412
show subpopulations
African (AFR)
AF:
0.0476
AC:
1980
AN:
41566
American (AMR)
AF:
0.162
AC:
2469
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.197
AC:
684
AN:
3470
East Asian (EAS)
AF:
0.0297
AC:
154
AN:
5186
South Asian (SAS)
AF:
0.112
AC:
543
AN:
4832
European-Finnish (FIN)
AF:
0.239
AC:
2531
AN:
10584
Middle Eastern (MID)
AF:
0.160
AC:
47
AN:
294
European-Non Finnish (NFE)
AF:
0.242
AC:
16477
AN:
67976
Other (OTH)
AF:
0.167
AC:
352
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1042
2084
3126
4168
5210
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
272
544
816
1088
1360
<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:
0.220
Hom.:
6035
Bravo
AF:
0.158
Asia WGS
AF:
0.0670
AC:
232
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
10
DANN
Benign
0.69
PhyloP100
0.40
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: rs4436830; hg19: chr17-28383709; API