rs764039253
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001282531.3(ADNP):c.3245_3247delATG(p.Asp1082del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
ADNP
NM_001282531.3 disruptive_inframe_deletion
NM_001282531.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.84
Publications
0 publications found
Genes affected
ADNP (HGNC:15766): (activity dependent neuroprotector homeobox) Vasoactive intestinal peptide is a neuroprotective factor that has a stimulatory effect on the growth of some tumor cells and an inhibitory effect on others. This gene encodes a protein that is upregulated by vasoactive intestinal peptide and may be involved in its stimulatory effect on certain tumor cells. The encoded protein contains one homeobox and nine zinc finger domains, suggesting that it functions as a transcription factor. This gene is also upregulated in normal proliferative tissues. Finally, the encoded protein may increase the viability of certain cell types through modulation of p53 activity. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]
ADNP Gene-Disease associations (from GenCC):
- ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorderInheritance: AD, Unknown Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Illumina, Orphanet, G2P, Labcorp Genetics (formerly Invitae), ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001282531.3. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001282531.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ADNP | MANE Select | c.3245_3247delATG | p.Asp1082del | disruptive_inframe_deletion | Exon 6 of 6 | NP_001269460.1 | Q9H2P0 | ||
| ADNP | c.3461_3463delATG | p.Asp1154del | disruptive_inframe_deletion | Exon 6 of 6 | NP_001425929.1 | ||||
| ADNP | c.3245_3247delATG | p.Asp1082del | disruptive_inframe_deletion | Exon 4 of 4 | NP_001269461.1 | Q9H2P0 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ADNP | TSL:5 MANE Select | c.3245_3247delATG | p.Asp1082del | disruptive_inframe_deletion | Exon 6 of 6 | ENSP00000483881.1 | Q9H2P0 | ||
| ADNP | TSL:1 | c.3245_3247delATG | p.Asp1082del | disruptive_inframe_deletion | Exon 4 of 4 | ENSP00000342905.3 | Q9H2P0 | ||
| ADNP | TSL:1 | c.3245_3247delATG | p.Asp1082del | disruptive_inframe_deletion | Exon 3 of 3 | ENSP00000360662.2 | Q9H2P0 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152224
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00000400 AC: 1AN: 250076 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
250076
AF XY:
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460418Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726598 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1460418
Hom.:
AF XY:
AC XY:
1
AN XY:
726598
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26130
East Asian (EAS)
AF:
AC:
0
AN:
39696
South Asian (SAS)
AF:
AC:
0
AN:
86248
European-Finnish (FIN)
AF:
AC:
0
AN:
52042
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111948
Other (OTH)
AF:
AC:
0
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
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2
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Allele balance
GnomAD4 genome 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152224
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74378
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41464
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5198
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68034
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
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0
1
1
2
2
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0.95
Allele balance
Alfa
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ClinVar
Not reported inComputational scores
Source:
Name
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PhyloP100
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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