rs979538866
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000503.6(EYA1):c.*866C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 151,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EYA1
NM_000503.6 3_prime_UTR
NM_000503.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.92
Publications
0 publications found
Genes affected
EYA1 (HGNC:3519): (EYA transcriptional coactivator and phosphatase 1) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may play a role in the developing kidney, branchial arches, eye, and ear. Mutations of this gene have been associated with branchiootorenal dysplasia syndrome, branchiootic syndrome, and sporadic cases of congenital cataracts and ocular anterior segment anomalies. A similar protein in mice can act as a transcriptional activator. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Dec 2013]
EYA1 Gene-Disease associations (from GenCC):
- branchio-oto-renal syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- branchiootorenal syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- branchiootic syndrome 1Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia
- branchiootic syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000503.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EYA1 | NM_000503.6 | MANE Select | c.*866C>T | 3_prime_UTR | Exon 18 of 18 | NP_000494.2 | |||
| EYA1 | NM_001370333.1 | c.*866C>T | 3_prime_UTR | Exon 19 of 19 | NP_001357262.1 | A0A2R8Y6K4 | |||
| EYA1 | NM_001370334.1 | c.*866C>T | 3_prime_UTR | Exon 20 of 20 | NP_001357263.1 | Q99502-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EYA1 | ENST00000340726.8 | TSL:1 MANE Select | c.*866C>T | 3_prime_UTR | Exon 18 of 18 | ENSP00000342626.3 | Q99502-1 | ||
| EYA1 | ENST00000388742.8 | TSL:1 | c.*866C>T | 3_prime_UTR | Exon 17 of 17 | ENSP00000373394.4 | Q99502-1 | ||
| EYA1 | ENST00000419131.6 | TSL:1 | c.*866C>T | 3_prime_UTR | Exon 16 of 16 | ENSP00000410176.1 | Q99502-3 |
Frequencies
GnomAD3 genomes 0.0000198 AC: 3AN: 151348Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151348
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 432Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 260
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
432
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
260
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
426
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
2
Other (OTH)
AF:
AC:
0
AN:
4
GnomAD4 genome 0.0000198 AC: 3AN: 151348Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73858 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151348
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
73858
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41174
American (AMR)
AF:
AC:
0
AN:
15200
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
0
AN:
4808
European-Finnish (FIN)
AF:
AC:
0
AN:
10290
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
2
AN:
67930
Other (OTH)
AF:
AC:
0
AN:
2076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Branchiootic syndrome 1 (1)
-
1
-
Otofaciocervical syndrome 1 (1)
Computational 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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