10-22960180-C-T

Position:

• chr10-22960180-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ARMC3	NM_173081.5	c.537+606C>T		intron_variant		ENST00000298032.10	NP_775104.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMC3	ENST00000298032.10	c.537+606C>T		intron_variant		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

Gnomad4 AFR exome AF: 0.186

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.220

Gnomad4 EAS exome AF: 0.0841

Gnomad4 SAS exome AF: 0.223

Gnomad4 FIN exome AF: 0.222

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.207

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

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.211

Alfa AF: 0.228 Hom.: 4340

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

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

Other links and lift over

dbSNP: rs11013210; hg19: chr10-23249109;