Variant 10-102006554-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_024541.3(ARMH3):c.1034C>T(p.Pro345Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00565 in 1,613,794 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0058 ( 36 hom. )

Consequence

ARMH3
NM_024541.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.33

Variant links:

Genes affected

ARMH3 (HGNC:25788): (armadillo like helical domain containing 3) Involved in regulation of Golgi organization. Located in Golgi membrane and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ARMH3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009393305).

BP6

Variant 10-102006554-G-A is Benign according to our data. Variant chr10-102006554-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640774.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMH3	NM_024541.3 linkuse as main transcript	c.1034C>T	p.Pro345Leu	missense_variant	14/26	ENST00000370033.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMH3	ENST00000370033.9 linkuse as main transcript	c.1034C>T	p.Pro345Leu	missense_variant	14/26	5	NM_024541.3	P1	Q5T2E6-1

Frequencies

GnomAD3 genomes

AF:

0.00419

AC:

637

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00452

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00670

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00451

AC:

1125

AN:

249504

Hom.:

AF XY:

0.00459

AC XY:

622

AN XY:

135366

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00287

Gnomad ASJ exome

AF:

0.0117

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.000928

Gnomad NFE exome

AF:

0.00718

Gnomad OTH exome

AF:

0.00694

GnomAD4 exome

AF:

0.00580

AC:

8482

AN:

1461522

Hom.:

Cov.:

AF XY:

0.00569

AC XY:

4139

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00322

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000522

Gnomad4 FIN exome

AF:

0.00116

Gnomad4 NFE exome

AF:

0.00676

Gnomad4 OTH exome

AF:

0.00562

GnomAD4 genome

AF:

0.00418

AC:

637

AN:

152272

Hom.:

Cov.:

AF XY:

0.00357

AC XY:

266

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00670

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00717

Hom.:

Bravo

AF:

0.00465

TwinsUK

AF:

0.00944

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.00231

AC:

ESP6500EA

AF:

0.00724

AC:

ExAC

AF:

0.00452

AC:

546

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00949

EpiControl

AF:

0.00788

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

Nov 01, 2022

ARMH3: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Uncertain

0.035

BayesDel_noAF

Pathogenic

0.28

Cadd

Pathogenic

Dann

Uncertain

0.98

DEOGEN2

Benign

0.047

Eigen

Benign

0.0051

Eigen_PC

Benign

0.18

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.98

M_CAP

Benign

0.0050

MetaRNN

Benign

0.0094

MetaSVM

Benign

-0.94

MutationTaster

Benign

1.0

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.23

Sift

Benign

0.081

Sift4G

Benign

0.31

Polyphen

0.014

Vest4

0.76

MVP

0.68

MPC

0.50

ClinPred

0.039

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.11

gMVP

0.41

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