11-72243769-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005169.4(PHOX2A):c.217+19C>A variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PHOX2A
NM_005169.4 intron
NM_005169.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.40
Publications
0 publications found
Genes affected
PHOX2A (HGNC:691): (paired like homeobox 2A) The protein encoded by this gene contains a paired-like homeodomain most similar to that of the Drosophila aristaless gene product. The encoded protein plays a central role in development of the autonomic nervous system. It regulates the expression of tyrosine hydroxylase and dopamine beta-hydroxylase, two catecholaminergic biosynthetic enzymes essential for the differentiation and maintenance of the noradrenergic neurotransmitter phenotype. The encoded protein has also been shown to regulate transcription of the alpha3 nicotinic acetylcholine receptor gene. Mutations in this gene have been associated with autosomal recessive congenital fibrosis of the extraocular muscles. [provided by RefSeq, Jul 2008]
PHOX2A Gene-Disease associations (from GenCC):
- fibrosis of extraocular muscles, congenital, 2Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
- congenital fibrosis of extraocular musclesInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 11-72243769-G-T is Benign according to our data. Variant chr11-72243769-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 259656.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005169.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1075782Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 510954
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1075782
Hom.:
Cov.:
21
AF XY:
AC XY:
0
AN XY:
510954
African (AFR)
AF:
AC:
0
AN:
22712
American (AMR)
AF:
AC:
0
AN:
8468
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14452
East Asian (EAS)
AF:
AC:
0
AN:
26474
South Asian (SAS)
AF:
AC:
0
AN:
24426
European-Finnish (FIN)
AF:
AC:
0
AN:
22016
Middle Eastern (MID)
AF:
AC:
0
AN:
2924
European-Non Finnish (NFE)
AF:
AC:
0
AN:
910774
Other (OTH)
AF:
AC:
0
AN:
43536
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (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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