chr10-23014324-T-A

Variant names:

• chr10-23014324-T-A
• rs1054052
• ENST00000409049.7:c.*203T>A

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ENSG00000286924 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ARMC3	NM_173081.5	c.2045+5393T>A		intron_variant	Intron 16 of 18	ENST00000298032.10	NP_775104.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMC3	ENST00000298032.10	c.2045+5393T>A		intron_variant	Intron 16 of 18	1	NM_173081.5	ENSP00000298032.5

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

African (AFR) AF: 0.331 AC: 9094 AN: 27494

American (AMR) AF: 0.573 AC: 12009 AN: 20962

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 11362 AN: 17452

East Asian (EAS) AF: 0.529 AC: 17254 AN: 32644

South Asian (SAS) AF: 0.608 AC: 35003 AN: 57554

European-Finnish (FIN) AF: 0.738 AC: 19128 AN: 25904

Middle Eastern (MID) AF: 0.669 AC: 3242 AN: 4848

European-Non Finnish (NFE) AF: 0.715 AC: 715126 AN: 1000654

Other (OTH) AF: 0.662 AC: 33441 AN: 50526

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

African (AFR) AF: 0.346 AC: 14340 AN: 41424

American (AMR) AF: 0.618 AC: 9433 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2250 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2790 AN: 5168

South Asian (SAS) AF: 0.603 AC: 2899 AN: 4810

European-Finnish (FIN) AF: 0.743 AC: 7847 AN: 10568

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48641 AN: 67932

Other (OTH) AF: 0.620 AC: 1309 AN: 2110

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
PhyloP100		1.6
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: rs1054052; hg19: chr10-23303253; COSMIC: COSV53065011;