Genetic Variant ARMC3:c.538-880C>T (chr10-22961004-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_173081.5(ARMC3):c.538-880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,076 control chromosomes in the GnomAD database, including 34,540 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 0.65 ( 34533 hom., cov: 31)

Exomes 𝑓: 0.56 ( 7 hom. )

Consequence

ARMC3
NM_173081.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0810

Publications

1 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:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173081.5. 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.538-880C>T	intron	N/A	NP_775104.2	Q5W041-2
ARMC3	NM_001282745.2		c.538-880C>T	intron	N/A	NP_001269674.1	Q5W041-4
ARMC3	NM_001282746.2		c.538-880C>T	intron	N/A	NP_001269675.1	Q5W041-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARMC3	ENST00000298032.10	TSL:1 MANE Select	c.538-880C>T	intron	N/A	ENSP00000298032.5	Q5W041-2
ARMC3	ENST00000409049.7	TSL:1	c.538-880C>T	intron	N/A	ENSP00000387288.3	Q5W041-3
ARMC3	ENST00000409983.7	TSL:2	c.538-880C>T	intron	N/A	ENSP00000386943.3	Q5W041-4

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99420

AN:

151906

Hom.:

34483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.908

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.626

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.617

GnomAD4 exome

AF:

0.558

AC:

AN:

Hom.:

Cov.:

AF XY:

0.611

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.655

AC:

99534

AN:

152024

Hom.:

34533

Cov.:

AF XY:

0.654

AC XY:

48539

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.908

AC:

37679

AN:

41502

American (AMR)

AF:

0.626

AC:

9571

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2052

AN:

3470

East Asian (EAS)

AF:

0.496

AC:

2557

AN:

5160

South Asian (SAS)

AF:

0.541

AC:

2602

AN:

4810

European-Finnish (FIN)

AF:

0.540

AC:

5696

AN:

10542

Middle Eastern (MID)

AF:

0.562

AC:

164

AN:

292

European-Non Finnish (NFE)

AF:

0.551

AC:

37445

AN:

67952

Other (OTH)

AF:

0.613

AC:

1291

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1593

3186

4779

6372

7965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.616

Hom.:

3568

Bravo

AF:

0.672

Asia WGS

AF:

0.516

AC:

1796

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.5

(source)

DANN

Benign

0.20

PhyloP100

0.081

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

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