rs1054052

chr10-23014324-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000409049.7(ARMC3):c.*203T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,389,984 control chromosomes in the GnomAD database, including 328,097 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 0.59 (28822 hom., cov: 30)
  • Exomes 𝑓: 0.69 (299275 hom.)
• Consequence: ARMC3 ENST00000409049.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARMC3	NM_173081.5	c.2045+5393T>A		intron_variant		ENST00000298032.10
LOC107984215	XR_001747394.2	n.555-18506A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARMC3	ENST00000298032.10	c.2045+5393T>A		intron_variant		1	NM_173081.5	A1
	ENST00000655462.1	n.117-48006A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90202 AN: 151828 Hom.: 28825 Cov.: 30

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.619

GnomAD4 exome AF: 0.691 AC: 855659 AN: 1238038 Hom.: 299275 Cov.: 42 AF XY: 0.690 AC XY: 413862 AN XY: 599982

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.573

Gnomad4 ASJ exome AF: 0.651

Gnomad4 EAS exome AF: 0.529

Gnomad4 SAS exome AF: 0.608

Gnomad4 FIN exome AF: 0.738

Gnomad4 NFE exome AF: 0.715

Gnomad4 OTH exome AF: 0.662

GnomAD4 genome AF: 0.594 AC: 90224 AN: 151946 Hom.: 28822 Cov.: 30 AF XY: 0.595 AC XY: 44178 AN XY: 74256

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.620

Alfa AF: 0.645 Hom.: 4136

Bravo AF: 0.571

Asia WGS AF: 0.582 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4
Dann	Benign	0.57

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: rs1054052; hg19: chr10-23303253; COSMIC: COSV53065011;