Variant chrX-101552945-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_016608.2(ARMCX1):c.15G>A(p.Arg5Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00475 in 1,208,561 control chromosomes in the GnomAD database, including 6 homozygotes. There are 1,815 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 0 hom., 76 hem., cov: 22)

Exomes 𝑓: 0.0049 ( 6 hom. 1739 hem. )

Consequence

ARMCX1
NM_016608.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.456

Variant links:

Genes affected

ARMCX1 (HGNC:18073): (armadillo repeat containing X-linked 1) This gene encodes a member of the ALEX family of proteins and may play a role in tumor suppression. The encoded protein contains a potential N-terminal transmembrane domain and two Armadillo (arm) repeats. Other proteins containing the arm repeat are involved in development, maintenance of tissue integrity, and tumorigenesis. This gene is closely localized with other family members, including ALEX2 and ALEX3, on the X chromosome. [provided by RefSeq, Jul 2008]

ARMCX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant X-101552945-G-A is Benign according to our data. Variant chrX-101552945-G-A is described in ClinVar as [Benign]. Clinvar id is 769182.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-101552945-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.456 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 76 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX1	NM_016608.2 link	c.15G>A	p.Arg5Arg	synonymous_variant	4/4	ENST00000372829.8	NP_057692.1	Q9P291A0A024RCI6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX1	ENST00000372829.8 link	c.15G>A	p.Arg5Arg	synonymous_variant	4/4	1	NM_016608.2	ENSP00000361917.3		Q9P291

Frequencies

GnomAD3 genomes

AF:

0.00305

AC:

342

AN:

112088

Hom.:

Cov.:

AF XY:

0.00219

AC XY:

AN XY:

34236

show subpopulations

Gnomad AFR

AF:

0.000648

Gnomad AMI

AF:

0.0117

Gnomad AMR

AF:

0.00558

Gnomad ASJ

AF:

0.00151

Gnomad EAS

AF:

0.000282

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000492

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00445

Gnomad OTH

AF:

0.00661

GnomAD3 exomes

AF:

0.00310

AC:

555

AN:

178777

Hom.:

AF XY:

0.00330

AC XY:

210

AN XY:

63607

show subpopulations

Gnomad AFR exome

AF:

0.000457

Gnomad AMR exome

AF:

0.00402

Gnomad ASJ exome

AF:

0.00155

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000764

Gnomad NFE exome

AF:

0.00490

Gnomad OTH exome

AF:

0.00588

GnomAD4 exome

AF:

0.00492

AC:

5399

AN:

1096419

Hom.:

Cov.:

AF XY:

0.00480

AC XY:

1739

AN XY:

361985

show subpopulations

Gnomad4 AFR exome

AF:

0.000531

Gnomad4 AMR exome

AF:

0.00430

Gnomad4 ASJ exome

AF:

0.00145

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000372

Gnomad4 FIN exome

AF:

0.000668

Gnomad4 NFE exome

AF:

0.00592

Gnomad4 OTH exome

AF:

0.00424

GnomAD4 genome

AF:

0.00306

AC:

343

AN:

112142

Hom.:

Cov.:

AF XY:

0.00222

AC XY:

AN XY:

34300

show subpopulations

Gnomad4 AFR

AF:

0.000647

Gnomad4 AMR

AF:

0.00557

Gnomad4 ASJ

AF:

0.00151

Gnomad4 EAS

AF:

0.000283

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000492

Gnomad4 NFE

AF:

0.00447

Gnomad4 OTH

AF:

0.00653

Alfa

AF:

0.00381

Hom.:

Bravo

AF:

0.00365

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

8.4

DANN

Benign

0.70

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