chr6-93361600-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004440.4(EPHA7):c.833-3189A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,852 control chromosomes in the GnomAD database, including 29,607 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 0.62 ( 29607 hom., cov: 32)
Consequence
EPHA7
NM_004440.4 intron
NM_004440.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.80
Publications
2 publications found
Genes affected
EPHA7 (HGNC:3390): (EPH receptor A7) This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Increased expression of this gene is associated with multiple forms of carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.624 AC: 94660AN: 151734Hom.: 29571 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
94660
AN:
151734
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.624 AC: 94740AN: 151852Hom.: 29607 Cov.: 32 AF XY: 0.624 AC XY: 46312AN XY: 74190 show subpopulations
GnomAD4 genome
AF:
AC:
94740
AN:
151852
Hom.:
Cov.:
32
AF XY:
AC XY:
46312
AN XY:
74190
show subpopulations
African (AFR)
AF:
AC:
27609
AN:
41468
American (AMR)
AF:
AC:
9878
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
2197
AN:
3460
East Asian (EAS)
AF:
AC:
3432
AN:
5168
South Asian (SAS)
AF:
AC:
2849
AN:
4828
European-Finnish (FIN)
AF:
AC:
6451
AN:
10550
Middle Eastern (MID)
AF:
AC:
169
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40192
AN:
67820
Other (OTH)
AF:
AC:
1282
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1852
3704
5557
7409
9261
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
770
1540
2310
3080
3850
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2084
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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