rs10518716
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024666.5(AAGAB):c.*336C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 235,686 control chromosomes in the GnomAD database, including 7,325 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 4128 hom., cov: 32)
Exomes 𝑓: 0.26 ( 3197 hom. )
Consequence
AAGAB
NM_024666.5 3_prime_UTR
NM_024666.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.163
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AAGAB | NM_024666.5 | c.*336C>G | 3_prime_UTR_variant | 10/10 | ENST00000261880.10 | ||
AAGAB | NM_001271885.2 | c.*336C>G | 3_prime_UTR_variant | 10/10 | |||
AAGAB | NM_001271886.2 | c.*336C>G | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AAGAB | ENST00000261880.10 | c.*336C>G | 3_prime_UTR_variant | 10/10 | 1 | NM_024666.5 | P1 | ||
AAGAB | ENST00000561452.5 | c.*336C>G | 3_prime_UTR_variant | 10/10 | 5 | ||||
AAGAB | ENST00000538028.1 | n.965C>G | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.213 AC: 32436AN: 151960Hom.: 4123 Cov.: 32
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GnomAD4 exome AF: 0.257 AC: 21496AN: 83608Hom.: 3197 Cov.: 0 AF XY: 0.258 AC XY: 11077AN XY: 43000
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GnomAD4 genome ? AF: 0.214 AC: 32470AN: 152078Hom.: 4128 Cov.: 32 AF XY: 0.218 AC XY: 16202AN XY: 74336
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at