rs11013210

Variant names:

• chr10-22960180-C-T
• rs11013210
• NM_173081.5:c.537+606C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173081.5(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 NM_173081.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 6 publications found

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMC3	NM_173081.5	c.537+606C>T		intron_variant	Intron 6 of 18	ENST00000298032.10	NP_775104.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMC3	ENST00000298032.10	c.537+606C>T		intron_variant	Intron 6 of 18	1	NM_173081.5	ENSP00000298032.5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32929 AN: 151762 Hom.: 3730 Cov.: 31

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.: 0 AF XY: 0.210 AC XY: 1832 AN XY: 8722

African (AFR) AF: 0.186 AC: 44 AN: 236

American (AMR) AF: 0.120 AC: 237 AN: 1982

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 70 AN: 318

East Asian (EAS) AF: 0.0841 AC: 57 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: 6 AN: 44

European-Non Finnish (NFE) AF: 0.235 AC: 2280 AN: 9686

Other (OTH) AF: 0.207 AC: 164 AN: 792

GnomAD4 genome AF: 0.217 AC: 32930 AN: 151880 Hom.: 3733 Cov.: 31 AF XY: 0.218 AC XY: 16181 AN XY: 74212

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: 59 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16557 AN: 67952

Other (OTH) AF: 0.211 AC: 445 AN: 2106

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11013210; hg19: chr10-23249109;