dbSNP rs1054052: ARMC3:c.*203T>A (chr10-23014324-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001282746.2(ARMC3):c.*203T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,389,984 control chromosomes in the GnomAD database, including 328,097 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 28822 hom., cov: 30)

Exomes 𝑓: 0.69 ( 299275 hom. )

Consequence

ARMC3
NM_001282746.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64

Publications

6 publications found

Variant links:

Genes affected

ARMC3 (HGNC:30964): (armadillo repeat containing 3) Armadillo/beta-catenin (CTNNB1; MIM 116806)-like (ARM) domains are imperfect 45-amino acid repeats involved in protein-protein interactions. ARM domain-containing proteins, such as ARMC3, function in signal transduction, development, cell adhesion and mobility, and tumor initiation and metastasis (Li et al., 2006 [PubMed 16915934]).[supplied by OMIM, Mar 2008]

ARMC3 links:

ENSG00000286924 (HGNC:):

ENSG00000286924 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001282746.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282746.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARMC3	NM_173081.5	MANE Select	c.2045+5393T>A	intron	N/A	NP_775104.2	Q5W041-2
ARMC3	NM_001282746.2		c.*203T>A	3_prime_UTR	Exon 17 of 17	NP_001269675.1	Q5W041-3
ARMC3	NM_001282745.2		c.2024+5393T>A	intron	N/A	NP_001269674.1	Q5W041-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARMC3	ENST00000409049.7	TSL:1	c.*203T>A	3_prime_UTR	Exon 17 of 17	ENSP00000387288.3	Q5W041-3
ARMC3	ENST00000298032.10	TSL:1 MANE Select	c.2045+5393T>A	intron	N/A	ENSP00000298032.5	Q5W041-2
ARMC3	ENST00000409983.7	TSL:2	c.2024+5393T>A	intron	N/A	ENSP00000386943.3	Q5W041-4

Frequencies

GnomAD3 genomes

AF:

0.594

AC:

90202

AN:

151828

Hom.:

28825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.648

Gnomad EAS

AF:

0.541

Gnomad SAS

AF:

0.602

Gnomad FIN

AF:

0.743

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.716

Gnomad OTH

AF:

0.619

GnomAD4 exome

AF:

0.691

AC:

855659

AN:

1238038

Hom.:

299275

Cov.:

AF XY:

0.690

AC XY:

413862

AN XY:

599982

show subpopulations

African (AFR)

AF:

0.331

AC:

9094

AN:

27494

American (AMR)

AF:

0.573

AC:

12009

AN:

20962

Ashkenazi Jewish (ASJ)

AF:

0.651

AC:

11362

AN:

17452

East Asian (EAS)

AF:

0.529

AC:

17254

AN:

32644

South Asian (SAS)

AF:

0.608

AC:

35003

AN:

57554

European-Finnish (FIN)

AF:

0.738

AC:

19128

AN:

25904

Middle Eastern (MID)

AF:

0.669

AC:

3242

AN:

4848

European-Non Finnish (NFE)

AF:

0.715

AC:

715126

AN:

1000654

Other (OTH)

AF:

0.662

AC:

33441

AN:

50526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

12703

25406

38109

50812

63515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19152

38304

57456

76608

95760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.594

AC:

90224

AN:

151946

Hom.:

28822

Cov.:

AF XY:

0.595

AC XY:

44178

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.346

AC:

14340

AN:

41424

American (AMR)

AF:

0.618

AC:

9433

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.648

AC:

2250

AN:

3470

East Asian (EAS)

AF:

0.540

AC:

2790

AN:

5168

South Asian (SAS)

AF:

0.603

AC:

2899

AN:

4810

European-Finnish (FIN)

AF:

0.743

AC:

7847

AN:

10568

Middle Eastern (MID)

AF:

0.673

AC:

198

AN:

294

European-Non Finnish (NFE)

AF:

0.716

AC:

48641

AN:

67932

Other (OTH)

AF:

0.620

AC:

1309

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1672

3345

5017

6690

8362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.645

Hom.:

4136

Bravo

AF:

0.571

Asia WGS

AF:

0.582

AC:

2023

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

(source)

DANN

Benign

0.57

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism (auto)

(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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over