Genetic Variant ATF7IP:p.Thr17Ala (chr12-14423964-A-G) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_018179.5(ATF7IP):c.49A>G(p.Thr17Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,459,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ATF7IP
NM_018179.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.18

Variant links:

Genes affected

ATF7IP (HGNC:20092): (activating transcription factor 7 interacting protein) ATF7IP is a multifunctional nuclear protein that associates with heterochromatin. It can act as a transcriptional coactivator or corepressor depending upon its binding partners (summary by Liu et al., 2009 [PubMed 19106100]).[supplied by OMIM, Nov 2010]

ATF7IP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.3896052).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATF7IP	NM_018179.5 link	c.49A>G	p.Thr17Ala	missense_variant	Exon 2 of 15	ENST00000261168.9	NP_060649.3	Q6VMQ6-1A0A024RAY1B3KNI7B3KQF8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATF7IP	ENST00000261168.9 link	c.49A>G	p.Thr17Ala	missense_variant	Exon 2 of 15	5	NM_018179.5	ENSP00000261168.4		Q6VMQ6-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000401

AC:

AN:

249564

Hom.:

AF XY:

0.00

AC XY:

AN XY:

134832

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000884

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1459810

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726080

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Oct 09, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.49A>G (p.T17A) alteration is located in exon 2 (coding exon 1) of the ATF7IP gene. This alteration results from a A to G substitution at nucleotide position 49, causing the threonine (T) at amino acid position 17 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.88

BayesDel_addAF

Uncertain

0.012

BayesDel_noAF

Benign

-0.22

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.14

T;T;.;.;T;T;T;.;T;T;T;T;.;T;T;.;T;T

Eigen

Pathogenic

0.74

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.91

D;D;D;D;.;D;D;D;D;D;D;D;D;D;D;D;D;.

M_CAP

Benign

0.034

MetaRNN

Benign

0.39

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.34

MutationAssessor

Benign

1.1

L;.;L;L;.;.;.;.;.;.;.;.;.;.;.;.;.;L

PrimateAI

Uncertain

0.61

PROVEAN

Benign

-1.2

N;D;N;N;D;D;D;N;D;D;D;D;D;N;D;D;D;N

REVEL

Uncertain

0.32

Sift

Pathogenic

0.0

D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D

Sift4G

Pathogenic

0.0

D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D

Polyphen

1.0

D;.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;D

Vest4

0.52

MutPred

0.34

Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);.;Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);Loss of phosphorylation at T17 (P = 0.0365);

MVP

0.54

MPC

0.65

ClinPred

0.82

GERP RS

5.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.29

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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