rs749694204
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_003924.4(PHOX2B):βc.735_761delβ(p.Ala252_Ala260del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000283 in 1,235,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β ). Synonymous variant affecting the same amino acid position (i.e. A245A) has been classified as Likely benign.
Frequency
Consequence
NM_003924.4 inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHOX2B | NM_003924.4 | c.735_761del | p.Ala252_Ala260del | inframe_deletion | 3/3 | ENST00000226382.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHOX2B | ENST00000226382.4 | c.735_761del | p.Ala252_Ala260del | inframe_deletion | 3/3 | 1 | NM_003924.4 | P1 | |
PHOX2B | ENST00000510424.2 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000477 AC: 7AN: 146666Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000465 AC: 1AN: 21500Hom.: 0 AF XY: 0.0000757 AC XY: 1AN XY: 13204
GnomAD4 exome AF: 0.0000257 AC: 28AN: 1089222Hom.: 0 AF XY: 0.0000249 AC XY: 13AN XY: 522656
GnomAD4 genome AF: 0.0000477 AC: 7AN: 146666Hom.: 0 Cov.: 32 AF XY: 0.0000841 AC XY: 6AN XY: 71376
ClinVar
Submissions by phenotype
Haddad syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at