20-50891435-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001282531.3(ADNP):c.3279C>T(p.Ala1093Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,610,974 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001282531.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000907 AC: 138AN: 152192Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000899 AC: 223AN: 248066Hom.: 0 AF XY: 0.000835 AC XY: 112AN XY: 134124
GnomAD4 exome AF: 0.00189 AC: 2753AN: 1458782Hom.: 6 Cov.: 35 AF XY: 0.00181 AC XY: 1313AN XY: 725706
GnomAD4 genome AF: 0.000907 AC: 138AN: 152192Hom.: 1 Cov.: 33 AF XY: 0.000659 AC XY: 49AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder Benign:1
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ADNP-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at