Variant chr20-50891355-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001282531.3(ADNP):c.*50A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 1,520,046 control chromosomes in the GnomAD database, including 661,873 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 68907 hom., cov: 34)

Exomes 𝑓: 0.93 ( 592966 hom. )

Consequence

ADNP
NM_001282531.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0810

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 20-50891355-T-G is Benign according to our data. Variant chr20-50891355-T-G is described in ClinVar as [Benign]. Clinvar id is 1189012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADNP	NM_001282531.3 linkuse as main transcript	c.*50A>C		3_prime_UTR_variant	6/6	ENST00000621696.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADNP	ENST00000621696.5 linkuse as main transcript	c.*50A>C		3_prime_UTR_variant	6/6	5	NM_001282531.3	P1

Frequencies

GnomAD3 genomes

AF:

0.951

AC:

144697

AN:

152224

Hom.:

68845

Cov.:

show subpopulations

Gnomad AFR

AF:

0.987

Gnomad AMI

AF:

0.925

Gnomad AMR

AF:

0.954

Gnomad ASJ

AF:

0.920

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.932

Gnomad FIN

AF:

0.953

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.927

Gnomad OTH

AF:

0.939

GnomAD3 exomes

AF:

0.946

AC:

145586

AN:

153852

Hom.:

68943

AF XY:

0.942

AC XY:

76148

AN XY:

80830

show subpopulations

Gnomad AFR exome

AF:

0.987

Gnomad AMR exome

AF:

0.968

Gnomad ASJ exome

AF:

0.910

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.931

Gnomad FIN exome

AF:

0.949

Gnomad NFE exome

AF:

0.927

Gnomad OTH exome

AF:

0.940

GnomAD4 exome

AF:

0.931

AC:

1273189

AN:

1367704

Hom.:

592966

Cov.:

AF XY:

0.931

AC XY:

626263

AN XY:

672884

show subpopulations

Gnomad4 AFR exome

AF:

0.988

Gnomad4 AMR exome

AF:

0.965

Gnomad4 ASJ exome

AF:

0.913

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.929

Gnomad4 FIN exome

AF:

0.948

Gnomad4 NFE exome

AF:

0.926

Gnomad4 OTH exome

AF:

0.933

GnomAD4 genome

AF:

0.951

AC:

144818

AN:

152342

Hom.:

68907

Cov.:

AF XY:

0.951

AC XY:

70866

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.987

Gnomad4 AMR

AF:

0.955

Gnomad4 ASJ

AF:

0.920

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.932

Gnomad4 FIN

AF:

0.953

Gnomad4 NFE

AF:

0.927

Gnomad4 OTH

AF:

0.939

Alfa

AF:

0.928

Hom.:

62236

Bravo

AF:

0.952

Asia WGS

AF:

0.976

AC:

3393

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.65

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over