Variant chrX-101489163-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The NM_001256155.3(ARMCX4):c.574A>T(p.Thr192Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000096 in 1,042,153 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 9.6e-7 ( 0 hom. 0 hem. )

Consequence

ARMCX4
NM_001256155.3 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.534

Variant links:

Genes affected

ARMCX4 (HGNC:28615): (armadillo repeat containing X-linked 4) The product of this gene belongs to the armadillo repeat-containing family of proteins, which interact with other proteins in a variety of cellular processes. The function of this family member is currently unknown. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ARMCX4 links:

ARMCX4 (HGNC:):

ARMCX4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.04796776).

BP6

Variant X-101489163-A-T is Benign according to our data. Variant chrX-101489163-A-T is described in ClinVar as [Benign]. Clinvar id is 208887.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX4	NM_001256155.3 linkuse as main transcript	c.574A>T	p.Thr192Ser	missense_variant	6/6	ENST00000423738.5	NP_001243084.2	Q5H9R4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX4	ENST00000423738.5 linkuse as main transcript	c.574A>T	p.Thr192Ser	missense_variant	6/6	5	NM_001256155.3	ENSP00000404304.3		Q5H9R4-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000998

AC:

AN:

100190

Hom.:

AF XY:

0.00

AC XY:

AN XY:

36808

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000519

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

9.60e-7

AC:

AN:

1042153

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

341229

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000358

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:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Abnormality of neuronal migration

Benign:1

Benign, no assertion criteria provided

clinical testing

Génétique et pathophysiologie de maladies neurodéveloppementales et épileptogènes, Institut de génétique et de biologie moléculaire et cellulaire

Oct 31, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.17

DANN

Benign

0.82

FATHMM_MKL

Benign

0.084

LIST_S2

Benign

0.27

M_CAP

Benign

0.018

MetaRNN

Benign

0.048

MetaSVM

Benign

-0.99

PrimateAI

Benign

0.28

REVEL

Benign

0.063

Sift4G

Benign

0.088

Vest4

0.060

MVP

0.37

ClinPred

0.027

GERP RS

-1.9

gMVP

0.065

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