dbSNP rs863223372: ARMCX4:p.Thr192Ser (chrX-101489163-A-T) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -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. 14/18 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

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -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 VariationId is 208887.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256155.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ARMCX4	NM_001256155.3	MANE Select	c.574A>T	p.Thr192Ser	missense	Exon 6 of 6	NP_001243084.2	Q5H9R4-1
ARMCX4	NR_028407.3		n.1381A>T		non_coding_transcript_exon	Exon 9 of 16
ARMCX4	NR_045861.2		n.1085A>T		non_coding_transcript_exon	Exon 6 of 13

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ARMCX4	ENST00000423738.5	TSL:5 MANE Select	c.574A>T	p.Thr192Ser	missense	Exon 6 of 6	ENSP00000404304.3	Q5H9R4-1
ARMCX4	ENST00000354842.5	TSL:1	n.574A>T		non_coding_transcript_exon	Exon 6 of 13	ENSP00000423927.2	A0A8J9A6E2
ARMCX4	ENST00000433011.6	TSL:1	n.574A>T		non_coding_transcript_exon	Exon 9 of 16	ENSP00000424452.2	A0A8J9A6E2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000998

AC:

AN:

100190

AF XY:

0.00

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 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

African (AFR)

AF:

0.00

AC:

AN:

24910

American (AMR)

AF:

0.0000358

AC:

AN:

27908

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18643

East Asian (EAS)

AF:

0.00

AC:

AN:

27134

South Asian (SAS)

AF:

0.00

AC:

AN:

49887

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25746

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4088

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

819523

Other (OTH)

AF:

0.00

AC:

AN:

44314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

Abnormality of neuronal migration (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.17

(source)

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

PhyloP100

-0.53

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

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over