11-72240115-GGCGCCCGCCGCGCCCGCC-GGCGCCCGCC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_005169.4(PHOX2A):c.480_488delGGCGGGCGC(p.Ala161_Ala163del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00269 in 1,532,060 control chromosomes in the GnomAD database, including 68 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005169.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHOX2A | NM_005169.4 | c.480_488delGGCGGGCGC | p.Ala161_Ala163del | disruptive_inframe_deletion | Exon 3 of 3 | ENST00000298231.5 | NP_005160.2 | |
PHOX2A | NM_001425096.1 | c.564_572delGGCGGGCGC | p.Ala189_Ala191del | disruptive_inframe_deletion | Exon 3 of 3 | NP_001412025.1 | ||
PHOX2A | NM_001425097.1 | c.504_512delGGCGGGCGC | p.Ala169_Ala171del | disruptive_inframe_deletion | Exon 3 of 3 | NP_001412026.1 | ||
PHOX2A | NM_001425098.1 | c.*359_*367delGGCGGGCGC | 3_prime_UTR_variant | Exon 3 of 3 | NP_001412027.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHOX2A | ENST00000298231.5 | c.480_488delGGCGGGCGC | p.Ala161_Ala163del | disruptive_inframe_deletion | Exon 3 of 3 | 1 | NM_005169.4 | ENSP00000298231.5 | ||
PHOX2A | ENST00000546310.1 | c.85-205_85-197delGGCGGGCGC | intron_variant | Intron 1 of 1 | 5 | ENSP00000444845.1 | ||||
PHOX2A | ENST00000544057.1 | n.348_356delGGCGGGCGC | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1927AN: 152044Hom.: 36 Cov.: 32
GnomAD3 exomes AF: 0.00255 AC: 327AN: 128204Hom.: 7 AF XY: 0.00218 AC XY: 153AN XY: 70294
GnomAD4 exome AF: 0.00159 AC: 2191AN: 1379906Hom.: 32 AF XY: 0.00142 AC XY: 969AN XY: 680766
GnomAD4 genome AF: 0.0127 AC: 1927AN: 152154Hom.: 36 Cov.: 32 AF XY: 0.0120 AC XY: 890AN XY: 74400
ClinVar
Submissions by phenotype
PHOX2A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at