rs757020181
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_003924.4(PHOX2B):βc.738_776delβ(p.Ala248_Ala260del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000636 in 1,288,314 control chromosomes in the GnomAD database, including 58 homozygotes. Variant has been reported in ClinVar as Likely benign (β β ). Synonymous variant affecting the same amino acid position (i.e. A246A) has been classified as Likely benign.
Frequency
Consequence
NM_003924.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHOX2B | NM_003924.4 | c.738_776del | p.Ala248_Ala260del | inframe_deletion | 3/3 | ENST00000226382.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHOX2B | ENST00000226382.4 | c.738_776del | p.Ala248_Ala260del | inframe_deletion | 3/3 | 1 | NM_003924.4 | P1 | |
PHOX2B | ENST00000510424.2 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000839 AC: 124AN: 147736Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00280 AC: 143AN: 51026Hom.: 26 AF XY: 0.00228 AC XY: 70AN XY: 30750
GnomAD4 exome AF: 0.000609 AC: 694AN: 1140466Hom.: 58 AF XY: 0.000620 AC XY: 342AN XY: 551168
GnomAD4 genome AF: 0.000845 AC: 125AN: 147848Hom.: 0 Cov.: 32 AF XY: 0.000903 AC XY: 65AN XY: 72020
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | PHOX2B: BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 14, 2019 | This variant is associated with the following publications: (PMID: 26375764) - |
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 08, 2017 | Other strong data supporting benign classification - |
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Oct 26, 2020 | - - |
Haddad syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at