chr15-67209444-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024666.5(AAGAB):c.618+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,601,580 control chromosomes in the GnomAD database, including 56,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.29 ( 6372 hom., cov: 32)
Exomes 𝑓: 0.26 ( 49643 hom. )
Consequence
AAGAB
NM_024666.5 intron
NM_024666.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.489
Genes affected
AAGAB (HGNC:25662): (alpha and gamma adaptin binding protein) The protein encoded by this gene interacts with the gamma-adaptin and alpha-adaptin subunits of complexes involved in clathrin-coated vesicle trafficking. Mutations in this gene are associated with type I punctate palmoplantar keratoderma. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
Variant 15-67209444-T-C is Benign according to our data. Variant chr15-67209444-T-C is described in ClinVar as [Benign]. Clinvar id is 1280017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AAGAB | NM_024666.5 | c.618+18A>G | intron_variant | ENST00000261880.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AAGAB | ENST00000261880.10 | c.618+18A>G | intron_variant | 1 | NM_024666.5 | P1 | |||
AAGAB | ENST00000542650.5 | c.291+18A>G | intron_variant | 2 | |||||
AAGAB | ENST00000561452.5 | c.291+18A>G | intron_variant | 5 | |||||
AAGAB | ENST00000538028.1 | n.299+18A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.287 AC: 43611AN: 151978Hom.: 6372 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
43611
AN:
151978
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:
GnomAD3 exomes AF: 0.288 AC: 71426AN: 247870Hom.: 10880 AF XY: 0.287 AC XY: 38604AN XY: 134504
GnomAD3 exomes
AF:
AC:
71426
AN:
247870
Hom.:
AF XY:
AC XY:
38604
AN XY:
134504
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.257 AC: 372969AN: 1449484Hom.: 49643 Cov.: 29 AF XY: 0.260 AC XY: 187952AN XY: 721834
GnomAD4 exome
AF:
AC:
372969
AN:
1449484
Hom.:
Cov.:
29
AF XY:
AC XY:
187952
AN XY:
721834
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.287 AC: 43630AN: 152096Hom.: 6372 Cov.: 32 AF XY: 0.289 AC XY: 21484AN XY: 74346
GnomAD4 genome
?
AF:
AC:
43630
AN:
152096
Hom.:
Cov.:
32
AF XY:
AC XY:
21484
AN XY:
74346
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1106
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Palmoplantar keratoderma, punctate type 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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