dbSNP rs11013210: ARMC3:c.537+606C>T (chr10-22960180-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 ENST00000298032.10(ARMC3):c.537+606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 168,330 control chromosomes in the GnomAD database, including 4,185 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 0.22 ( 3733 hom., cov: 31)

Exomes 𝑓: 0.21 ( 452 hom. )

Consequence

ARMC3
ENST00000298032.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.575

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:

Genome browser will be placed here

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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000298032.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ARMC3	NM_173081.5	MANE Select	c.537+606C>T	intron	N/A	NP_775104.2
ARMC3	NM_001282745.2		c.537+606C>T	intron	N/A	NP_001269674.1
ARMC3	NM_001282746.2		c.537+606C>T	intron	N/A	NP_001269675.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ARMC3	ENST00000298032.10	TSL:1 MANE Select	c.537+606C>T	intron	N/A	ENSP00000298032.5
ARMC3	ENST00000409049.7	TSL:1	c.537+606C>T	intron	N/A	ENSP00000387288.3
ARMC3	ENST00000464017.1	TSL:2	n.885C>T	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32929

AN:

151762

Hom.:

3730

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.210

GnomAD4 exome

AF:

0.211

AC:

3463

AN:

16450

Hom.:

452

Cov.:

AF XY:

0.210

AC XY:

1832

AN XY:

8722

show subpopulations

African (AFR)

AF:

0.186

AC:

AN:

236

American (AMR)

AF:

0.120

AC:

237

AN:

1982

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

AN:

318

East Asian (EAS)

AF:

0.0841

AC:

AN:

678

South Asian (SAS)

AF:

0.223

AC:

478

AN:

2142

European-Finnish (FIN)

AF:

0.222

AC:

127

AN:

572

Middle Eastern (MID)

AF:

0.136

AC:

AN:

European-Non Finnish (NFE)

AF:

0.235

AC:

2280

AN:

9686

Other (OTH)

AF:

0.207

AC:

164

AN:

792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

128

255

383

510

638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.217

AC:

32930

AN:

151880

Hom.:

3733

Cov.:

AF XY:

0.218

AC XY:

16181

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.186

AC:

7698

AN:

41388

American (AMR)

AF:

0.164

AC:

2510

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.261

AC:

906

AN:

3468

East Asian (EAS)

AF:

0.119

AC:

616

AN:

5160

South Asian (SAS)

AF:

0.234

AC:

1126

AN:

4810

European-Finnish (FIN)

AF:

0.256

AC:

2691

AN:

10530

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16557

AN:

67952

Other (OTH)

AF:

0.211

AC:

445

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1293

2586

3879

5172

6465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.225

Hom.:

6029

Bravo

AF:

0.206

Asia WGS

AF:

0.195

AC:

676

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.6

(source)

DANN

Benign

0.78

PhyloP100

-0.57

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