Variant X-101615970-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 ENST00000361910.9(ARMCX6):c.651C>T(p.Ala217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00088 ( 0 hom., 2 hem., cov: 7)

Exomes 𝑓: 0.0014 ( 2 hom. 188 hem. )

Consequence

ARMCX6
ENST00000361910.9 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.45

Variant links:

Genes affected

ARMCX6 (HGNC:26094): (armadillo repeat containing X-linked 6) Predicted to be located in mitochondrial outer membrane. Predicted to be integral component of membrane. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ARMCX6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant X-101615970-G-A is Benign according to our data. Variant chrX-101615970-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661066.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.45 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX6	NM_019007.4 linkuse as main transcript	c.651C>T	p.Ala217=	synonymous_variant	3/3	ENST00000361910.9	NP_061880.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX6	ENST00000361910.9 linkuse as main transcript	c.651C>T	p.Ala217=	synonymous_variant	3/3	1	NM_019007.4	ENSP00000354708	P1

Frequencies

GnomAD3 genomes

AF:

0.000875

AC:

AN:

51414

Hom.:

Cov.:

AF XY:

0.000650

AC XY:

AN XY:

3078

show subpopulations

Gnomad AFR

AF:

0.0000799

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000502

Gnomad ASJ

AF:

0.00140

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00171

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00131

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000704

AC:

AN:

53957

Hom.:

AF XY:

0.000589

AC XY:

AN XY:

15269

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000207

Gnomad ASJ exome

AF:

0.00127

Gnomad EAS exome

AF:

0.000323

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00170

Gnomad NFE exome

AF:

0.00108

Gnomad OTH exome

AF:

0.00119

GnomAD4 exome

AF:

0.00139

AC:

713

AN:

514657

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

188

AN XY:

145799

show subpopulations

Gnomad4 AFR exome

AF:

0.0000746

Gnomad4 AMR exome

AF:

0.000235

Gnomad4 ASJ exome

AF:

0.00139

Gnomad4 EAS exome

AF:

0.0000409

Gnomad4 SAS exome

AF:

0.000483

Gnomad4 FIN exome

AF:

0.00123

Gnomad4 NFE exome

AF:

0.00167

Gnomad4 OTH exome

AF:

0.00151

GnomAD4 genome

AF:

0.000875

AC:

AN:

51411

Hom.:

Cov.:

AF XY:

0.000645

AC XY:

AN XY:

3099

show subpopulations

Gnomad4 AFR

AF:

0.0000797

Gnomad4 AMR

AF:

0.000501

Gnomad4 ASJ

AF:

0.00140

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00171

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000682

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

ARMCX6: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

2.3

DANN

Benign

0.76

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