rs577498739
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBS1BS2
The NM_001282531.3(ADNP):c.422_424dupGCA(p.Ser141dup) variant causes a conservative inframe insertion change. The variant allele was found at a frequency of 0.00388 in 1,613,890 control chromosomes in the GnomAD database, including 28 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001282531.3 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00250 AC: 381AN: 152196Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00230 AC: 577AN: 251090Hom.: 1 AF XY: 0.00218 AC XY: 296AN XY: 135702
GnomAD4 exome AF: 0.00402 AC: 5878AN: 1461576Hom.: 27 Cov.: 34 AF XY: 0.00397 AC XY: 2886AN XY: 727094
GnomAD4 genome AF: 0.00250 AC: 381AN: 152314Hom.: 1 Cov.: 32 AF XY: 0.00231 AC XY: 172AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:3
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ADNP: PM4:Supporting, BS1, BS2 -
ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder 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 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