rs1171136

chr10-22935933-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.48+3889C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,994 control chromosomes in the GnomAD database, including 15,938 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 0.40 (15938 hom., cov: 32)
• Consequence: ARMC3 NM_173081.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC3	NM_173081.5	c.48+3889C>T		intron_variant		ENST00000298032.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC3	ENST00000298032.10	c.48+3889C>T		intron_variant		1	NM_173081.5	A1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60876 AN: 151876 Hom.: 15889 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.378

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.401 AC: 60980 AN: 151994 Hom.: 15938 Cov.: 32 AF XY: 0.399 AC XY: 29635 AN XY: 74304

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.376

Alfa AF: 0.340 Hom.: 1869

Bravo AF: 0.436

Asia WGS AF: 0.406 AC: 1411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.5
Dann	Benign	0.12

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: rs1171136; hg19: chr10-23224862;